WO2015051251A1 - A tor kinase inhibitor in the prevention or treatment of cancer characterized by gene mutations - Google Patents

A tor kinase inhibitor in the prevention or treatment of cancer characterized by gene mutations Download PDF

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Publication number
WO2015051251A1
WO2015051251A1 PCT/US2014/059043 US2014059043W WO2015051251A1 WO 2015051251 A1 WO2015051251 A1 WO 2015051251A1 US 2014059043 W US2014059043 W US 2014059043W WO 2015051251 A1 WO2015051251 A1 WO 2015051251A1
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gene
mutation
patient
tor kinase
kinase inhibitor
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PCT/US2014/059043
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English (en)
French (fr)
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Shuichan Xu
Kristen Mae HEGE
Xiaoling Wu
Zhihong Yang
Konstantinos Mavrommatis
Ellen Filvaroff
Tao Shi
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Signal Pharmaceuticals, Llc
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Priority to EP14795888.8A priority Critical patent/EP3052093A1/en
Priority to MX2016004212A priority patent/MX2016004212A/es
Priority to CN201480066619.0A priority patent/CN105792816A/zh
Priority to JP2016519822A priority patent/JP2016540726A/ja
Publication of WO2015051251A1 publication Critical patent/WO2015051251A1/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/4985—Pyrazines or piperazines ortho- or peri-condensed with heterocyclic ring systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P15/00—Drugs for genital or sexual disorders; Contraceptives
    • A61P15/08—Drugs for genital or sexual disorders; Contraceptives for gonadal disorders or for enhancing fertility, e.g. inducers of ovulation or of spermatogenesis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism

Definitions

  • a cancer in a patient comprising administering an effective amount of a TOR kinase inhibitor to a patient having cancer, in particular breast cancer, diffuse large B-cell lymphoma, glioblastoma multiforme, hepatocellular carcinoma, multiple myeloma, neuroendocrine tumor, or non-small cell lung cancer, characterized by particular gene mutation(s) or variant(s) relative to the genes of a biological wild-type sample.
  • cancer in particular breast cancer, diffuse large B-cell lymphoma, glioblastoma multiforme, hepatocellular carcinoma, multiple myeloma, neuroendocrine tumor, or non-small cell lung cancer, characterized by particular gene mutation(s) or variant(s) relative to the genes of a biological wild-type sample.
  • the protein kinases belong to a large and diverse family of enzymes that catalyze protein phosphorylation and play a critical role in cellular signaling. Protein kinases may exert positive or negative regulatory effects, depending upon their target protein. Protein kinases are involved in specific signaling pathways which regulate cell functions such as, but not limited to, metabolism, cell cycle progression, cell adhesion, vascular function, apoptosis, and angiogenesis.
  • mTOR mammalian target of rapamycin
  • FRAP FRAP
  • RAFTI or RAPT1 is a 2549-amino acid Ser/Thr protein kinase, that has been shown to be one of the most critical proteins in the mTOR/PBK/Akt pathway that regulates cell growth and proliferation. Georgakis and Younes Expert Rev. Anticancer Ther. 6(1): 131-140 (2006). mTOR exists within two complexes, mTORCl and mTORC2. While mTORCl is sensitive to rapamycin analogs (such as temsirolimus or everolimus), mTORC2 is largely rapamycin-insensitive.
  • rapamycin is not a TOR kinase inhibitor.
  • mTOR inhibitors have been or are being evaluated in clinical trials for the treatment of cancer. Temsirolimus was approved for use in renal cell carcinoma in 2007 and everolimus was approved in 2009 for renal cell carcinoma patients that have progressed on vascular endothelial growth factor receptor inhibitors. In addition, sirolimus was approved in 1999 for the prophylaxis of renal transplant rejection.
  • the interesting but limited clinical success of these mTORCl inhibitory compounds demonstrates the usefulness of mTOR inhibitors in the treatment of cancer and transplant rejection, and the increased potential for compounds with both mTORC 1 and mTORC2 inhibitory activity.
  • identification of specific mutations associated with breast cancer may lead to improved therapeutic protocols.
  • a cancer characterized by a gene mutation for example, breast cancer
  • methods for treating or preventing a cancer characterized by a gene mutation comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a particular gene mutation, relative to wild type.
  • a TOR kinase inhibitor for example, breast cancer
  • a cancer characterized by a gene mutation for example breast cancer
  • methods for treating or preventing a cancer characterized by a gene mutation comprising screening a patient's cancer for the presence of a particular gene mutation relative to wild type, and administering an effective amount of a TOR kinase inhibitor to the patient having a cancer characterized by a particular gene mutation.
  • TOR kinase inhibitor in a patient having a cancer characterized by a gene mutation, for example breast cancer comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of one or more genes selected from Table 1 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of a mutation indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • TOR kinase inhibitor treatment of a patient having a cancer characterized by a gene mutation, for example breast cancer with a TOR kinase inhibitor
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence(s) of one or more genes selected from Table 1 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of a mutation indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • a cancer characterized by one or more gene variants for example, breast cancer, diffuse large B-cell lymphoma (DLBCL), glioblastoma multiforme (GBM), hepatocellular carcinoma (HCC), multiple myeloma (MM), neuroendocrine tumor (NET), or non-small cell lung cancer (NSCLC), comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by one or more particular gene variants, relative to wild type.
  • DLBCL diffuse large B-cell lymphoma
  • GBM glioblastoma multiforme
  • HCC hepatocellular carcinoma
  • MM multiple myeloma
  • NET neuroendocrine tumor
  • NSCLC non-small cell lung cancer
  • a cancer characterized by one or more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, comprising screening a patient's cancer for the presence of one or more particular gene variants relative to wild type, and administering an effective amount of a TOR kinase inhibitor to the patient having a cancer characterized by one or more particular gene variants.
  • TOR kinase inhibitor in a patient having a cancer characterized by one or more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of the genes listed in Fig. 2 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants in one or more genes selected from Fig. 2, Table 2, or Table 3 indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • TOR kinase inhibitor in a patient having a cancer characterized by one or more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of one or more genes selected from Table 2 or Table 3 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • TOR kinase inhibitor treatment of a patient having a cancer characterized by one ore more gene variants, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, with a TOR kinase inhibitor
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence(s) of the genes listed in Fig. 2 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants of one or more genes selected from Fig. 2, Table 2 or Table 3 indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • TOR kinase inhibitor treatment of a patient having a cancer characterized by one ore more gene variants, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, with a TOR kinase inhibitor
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence(s) of one or more genes selected from Table 2 or Table 3 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • the TOR kinase inhibitor is a compound as described herein.
  • FIG 1. provides a patient disposition overview, showing treatment duration, dose modifications, and best RECIST (with target lesion response) for patients treated with
  • Compound 1 (data as of September 2014). Signals of Compound 1 clinical activity were demonstrated with 3/17 target lesions showing PR (2/17 showing RECIST PR), all with PIK3CA mutations, in addition to mutations in RICTOR, TP53, IGF1R and/or PTEN. Additionally, mutations in BRCA2, ARID 1 A, FGFR1, FGFR and PTPRD were observed.
  • FIG. 2. provides the list of genes evaluated for variants compared to wild type.
  • FIGs 3A-3C. provides a patient disposition overview, showing treatment duration, compound combination and dose modifications, EGFR mutation status, survival (in weeks) and best RECIST (with target lesion response) for NSCLC patients treated with
  • FIG. 4. shows that low IRF4 gene expression levels correlate with sensitivity to
  • FIG. 5. shows that low IRF4 protein expression levels correlate with sensitivity to
  • Compound 1 Compound 1; x-axis: IRF4 protein expression level as measured by RPPA.
  • FIG. 6 shows that the sensitivity to Compound 1 correlates with activation of mTORCl and mTORC2 in a subgroup of DLBCL cell lines as measured via biomarker expression (p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, pS6 S240/S244 and S235/S236) using RPPA.
  • the level of each biomarker in each DLBCL line is shown in a heatmap (dark gray: high; light gray: low).
  • Compound 1 are shown at the top of the heatmap (light gray: low; dark gray: high).
  • alkyl group is a saturated, partially saturated, or unsaturated straight chain or branched non-cyclic hydrocarbon having from 1 to 10 carbon atoms, typically from 1 to 8 carbons or, in some embodiments, from 1 to 6, 1 to 4, or 2 to 6 or carbon atoms.
  • Representative alkyl groups include -methyl, -ethyl, -n-propyl, -n-butyl, -n-pentyl and -n-hexyl; while saturated branched alkyls include -isopropyl, -sec-butyl, -isobutyl, -tert-butyl, -isopentyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl, 2,3-dimethylbutyl and the like.
  • An alkyl group can be substituted or unsubstituted.
  • alkyl groups described herein when they are said to be "substituted,” they may be substituted with any substituent or substituents as those found in the exemplary compounds and embodiments disclosed herein, as well as halogen (chloro, iodo, bromo, or fluoro); alkyl; hydroxyl; alkoxy; alkoxyalkyl; amino; alkylamino; carboxy; nitro;
  • cyano; thiol; thioether; imine; imide; amidine; guanidine; enamine; aminocarbonyl; acylamino; phosphonate; phosphine; thiocarbonyl; sulfmyl; sulfone; sulfonamide; ketone; aldehyde; ester; urea; urethane; oxime; hydroxyl amine; alkoxyamine; aryloxyamine; aralkoxy amine; N-oxide; hydrazine; hydrazide; hydrazone; azide; isocyanate; isothiocyanate; cyanate; thiocyanate; oxygen ( 0); B(OH)2, or 0(alkyl)aminocarbonyl.
  • An "alkenyl” group is a straight chain or branched non-cyclic hydrocarbon having from 2 to 10 carbon atoms, typically from 2 to 8 carbon atoms, and including at least one carbon-carbon double bond.
  • Representative straight chain and branched (C 2 -Cg)alkenyls include -vinyl, -allyl, -1-butenyl, -2-butenyl, -isobutylenyl, -1-pentenyl, -2-pentenyl, -3 -methyl- 1- butenyl, -2-methyl-2-butenyl, -2,3-dimethyl-2-butenyl, -1-hexenyl, -2-hexenyl, -3-hexenyl, -1-heptenyl, -2-heptenyl, -3-heptenyl, -1-octenyl, -2-octenyl, -3-octenyl and the like.
  • a "cycloalkyl” group is a saturated, or partially saturated cyclic alkyl group of from 3 to 10 carbon atoms having a single cyclic ring or multiple condensed or bridged rings which can be optionally substituted with from 1 to 3 alkyl groups.
  • the cycloalkyl group has 3 to 8 ring members, whereas in other embodiments the number of ring carbon atoms ranges from 3 to 5, 3 to 6, or 3 to 7.
  • Such cycloalkyl groups include, by way of example, single ring structures such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, 1-methylcyclopropyl, 2-methylcyclopentyl, 2-methylcyclooctyl, and the like, or multiple or bridged ring structures such as adamantyl and the like.
  • Examples of unsaturared cycloalkyl groups include cyclohexenyl, cyclopentenyl, cyclohexadienyl, butadienyl, pentadienyl, hexadienyl, among others.
  • a cycloalkyl group can be substituted or unsubstituted.
  • substituted cycloalkyl groups include, by way of example, cyclohexanone and the like.
  • aryl group is an aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring (e.g., phenyl) or multiple condensed rings (e.g., naphthyl or anthryl). In some embodiments, aryl groups contain 6-14 carbons, and in others from 6 to 12 or even 6 to 10 carbon atoms in the ring portions of the groups. Particular aryls include phenyl, biphenyl, naphthyl and the like. An aryl group can be substituted or unsubstituted. The phrase "aryl groups” also includes groups containing fused rings, such as fused aromatic-aliphatic ring systems (e.g., indanyl, tetrahydronaphthyl, and the like).
  • a "heteroaryl” group is an aryl ring system having one to four heteroatoms as ring atoms in a heteroaromatic ring system, wherein the remainder of the atoms are carbon atoms.
  • heteroaryl groups contain 5 to 6 ring atoms, and in others from 6 to 9 or even 6 to 10 atoms in the ring portions of the groups. Suitable heteroatoms include oxygen, sulfur and nitrogen.
  • the heteroaryl ring system is monocyclic or bicyclic.
  • Non- limiting examples include but are not limited to, groups such as pyrrolyl, pyrazolyl, imidazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, pyrolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, thiophenyl, benzothiophenyl, furanyl, benzofuranyl (for example, isobenzofuran-1 ,3- diimine), indolyl, azaindolyl (for example, pyrrolopyridyl or lH-pyrrolo[2,3-b]pyridyl), indazolyl, benzimidazolyl (for example, lH-benzo[d]imidazolyl), imidazopyridyl (for example, azabenzimidazolyl, 3H-imidazo[4,5-b
  • heterocyclyl is an aromatic (also referred to as heteroaryl) or non-aromatic cycloalkyl in which one to four of the ring carbon atoms are independently replaced with a heteroatom from the group consisting of O, S and N.
  • heterocyclyl groups include 3 to 10 ring members, whereas other such groups have 3 to 5, 3 to 6, or 3 to 8 ring members.
  • Heterocyclyls can also be bonded to other groups at any ring atom (i.e., at any carbon atom or heteroatom of the heterocyclic ring).
  • a heterocyclylalkyl group can be substituted or unsubstituted.
  • Heterocyclyl groups encompass unsaturated, partially saturated and saturated ring systems, such as, for example, imidazolyl, imidazolinyl and imidazolidinyl groups.
  • heterocyclyl includes fused ring species, including those comprising fused aromatic and non-aromatic groups, such as, for example, benzotriazolyl, 2,3-dihydrobenzo[l,4]dioxinyl, and benzo[l,3]dioxolyl.
  • the phrase also includes bridged polycyclic ring systems containing a heteroatom such as, but not limited to, quinuclidyl.
  • heterocyclyl group examples include, but are not limited to, aziridinyl, azetidinyl, pyrrolidyl, imidazolidinyl, pyrazolidinyl, thiazolidinyl, tetrahydrothiophenyl, tetrahydrofuranyl, dioxolyl, furanyl, thiophenyl, pyrrolyl, pyrrolinyl, imidazolyl, imidazolinyl, pyrazolyl, pyrazolinyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, thiazolinyl, isothiazolyl, thiadiazolyl, oxadiazolyl, piperidyl, piperazinyl, morpholinyl, thiomorpholinyl, tetrahydropyranyl (for example, tetrahydro- 2
  • substituted heterocyclyl groups may be mono- substituted or substituted more than once, such as, but not limited to, pyridyl or morpholinyl groups, which are 2-, 3-, 4-, 5-, or 6-substituted, or disubstituted with various substituents such as those listed below.
  • cycloalkylalkyl is a radical of the formula: -alkyl-cycloalkyl, wherein alkyl and cycloalkyl are defined above. Substituted cycloalkylalkyl groups may be substituted at the alkyl, the cycloalkyl, or both the alkyl and the cycloalkyl portions of the group.
  • Representative cycloalkylalkyl groups include but are not limited to cyclopentylmethyl, cyclopentylethyl, cyclohexylmethyl, cyclohexylethyl, and cyclohexylpropyl.
  • Representative substituted cycloalkylalkyl groups may be mono- substituted or substituted more than once.
  • An "aralkyl” group is a radical of the formula: -alkyl-aryl, wherein alkyl and aryl are defined above. Substituted aralkyl groups may be substituted at the alkyl, the aryl, or both the alkyl and the aryl portions of the group. Representative aralkyl groups include but are not limited to benzyl and phenethyl groups and fused (cycloalkylaryl)alkyl groups such as 4-ethyl-indanyl.
  • heterocyclylalkyl is a radical of the formula: -alkyl-heterocyclyl, wherein alkyl and heterocyclyl are defined above. Substituted heterocyclylalkyl groups may be substituted at the alkyl, the heterocyclyl, or both the alkyl and the heterocyclyl portions of the group.
  • heterocylylalkyl groups include but are not limited to 4-ethyl-morpholinyl, 4-propylmorpholinyl, furan-2-yl methyl, furan-3-yl methyl, pyrdine-3-yl methyl, (tetrahydro-2H- pyran-4-yl)methyl, (tetrahydro-2H-pyran-4-yl)ethyl, tetrahydrofuran-2-yl methyl,
  • a "halogen” is chloro, iodo, bromo, or fluoro.
  • a "hydroxyalkyl” group is an alkyl group as described above substituted with one or more hydroxy groups.
  • alkoxy is -O-(alkyl), wherein alkyl is defined above.
  • alkoxyalkyl is -(alkyl)-O-(alkyl), wherein alkyl is defined above.
  • An "amine” group is a radical of the formula: -NH 2 .
  • a "hydroxyl amine” group is a radical of the formula: -N(R )OH or -NHOH, wherein R is a substituted or unsubstituted alkyl, cycloalkyl, cycloalkylalkyl, aryl, aralkyl, heterocyclyl or heterocyclylalkyl group as defined herein.
  • An "alkoxyamine” group is a radical of the formula: -N(R )0-alkyl or -NHO-alkyl, wherein R is as defined above.
  • aryloxyamine is a radical of the formula: -N(R )0-aryl or -NHO-aryl, wherein R is as defined above
  • An "aralkoxyamine” group is a radical of the formula: -N(R )0-aralkyl or -NHO-aralkyl, wherein R is as defined above.
  • alkylamine is a radical of the formula: -NH-alkyl or -N(alkyl) 2 , wherein each alkyl is independently as defined above.
  • An "0(alkyl)aminocarbonyl” group is a radical of the formula:
  • each R is independently as defined above.
  • N-oxide group is a radical of the formula: -N -O " .
  • each R is independently as defined above.
  • An "amidine” group is a radical of the formula: -
  • each R is independently as defined above.
  • a "hydrazine” group is a radical of the formula: -N(R)N(R) 2 , -NHN(R) 2 ,
  • each R is independently as defined above.
  • An "azide” group is a radical of the formula: -N 3 .
  • a "cyanate” group is a radical of the formula: -OCN.
  • a "thiocyanate” group is a radical of the formula: -SCN.
  • a "thioether” group is a radical of the formula; -S(R ), wherein R is as defined above.
  • a "sulfonylamino" group is a radical of the formula: -NHS0 2 (R ) or
  • each R is independently as defined above.
  • each R is independently as defined above.
  • a "phosphine” group is a radical of the formula: -P(R ) 2 , wherein each R is independently as defined above.
  • substituted they may be substituted with any appropriate substituent or substituents.
  • pyrrolidyl piperidyl, piperazinyl, morpholinyl, or thiazinyl
  • monocyclic or fused or non- fused polycyclic aryl or heteroaryl e.g., phenyl, naphthyl, pyrrolyl, indolyl, furanyl, thiophenyl, imidazolyl, oxazolyl, isoxazolyl, thiazolyl, triazolyl, tetrazolyl, pyrazolyl, pyridinyl, quinolinyl, isoquinolinyl, acridinyl, pyrazinyl, pyridazinyl, pyrimidinyl, benzimidazolyl, benzothiophenyl, or benzofuranyl) aryloxy; aralkyloxy; heterocyclyloxy; and heterocyclyl alkoxy.
  • the term "pharmaceutically acceptable salt(s)” refers to a salt prepared from a pharmaceutically acceptable non-toxic acid or base including an inorganic acid and base and an organic acid and base.
  • Suitable pharmaceutically acceptable base addition salts of the TOR kinase inhibitors include, but are not limited to metallic salts made from aluminum, calcium, lithium, magnesium, potassium, sodium and zinc or organic salts made from lysine, ⁇ , ⁇ '-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, ethylenediamine, meglumine (N-methylglucamine) and procaine.
  • Suitable non-toxic acids include, but are not limited to, inorganic and organic acids such as acetic, alginic, anthranilic, benzenesulfonic, benzoic, camphorsulfonic, citric, ethenesulfonic, formic, fumaric, furoic, galacturonic, gluconic, glucuronic, glutamic, glycolic, hydrobromic, hydrochloric, isethionic, lactic, maleic, malic, mandelic, methanesulfonic, mucic, nitric, pamoic, pantothenic, phenylacetic, phosphoric, propionic, salicylic, stearic, succinic, sulfanilic, sulfuric, tartaric acid, and p-toluenesulfonic acid.
  • Specific non-toxic acids include hydrochloric, hydrobromic, phosphoric, sulfuric, and
  • methanesulfonic acids examples include hydrochloride and mesylate salts.
  • Others are well-known in the art, see for example, Remington 's Pharmaceutical Sciences, 18 th eds., Mack Publishing, Easton PA (1990) or Remington: The Science and Practice of
  • the term “clathrate” means a TOR kinase inhibitor, or a salt thereof, in the form of a crystal lattice that contains spaces (e.g., channels) that have a guest molecule (e.g. , a solvent or water) trapped within or a crystal lattice wherein a TOR kinase inhibitor is a guest molecule.
  • the term “solvate” means a TOR kinase inhibitor, or a salt thereof, that further includes a stoichiometric or non-stoichiometric amount of a solvent bound by non-covalent intermolecular forces. In one embodiment, the solvate is a hydrate.
  • hydrate means a TOR kinase inhibitor, or a salt thereof, that further includes a stoichiometric or non-stoichiometric amount of water bound by non-covalent intermolecular forces.
  • prodrug means a TOR kinase inhibitor derivative that can hydrolyze, oxidize, or otherwise react under biological conditions (in vitro or in vivo) to provide an active compound, particularly a TOR kinase inhibitor.
  • prodrugs include, but are not limited to, derivatives and metabolites of a TOR kinase inhibitor that include biohydrolyzable moieties such as biohydrolyzable amides, biohydrolyzable esters, biohydrolyzable carbamates, biohydrolyzable carbonates, biohydrolyzable ureides, and biohydrolyzable phosphate analogues.
  • prodrugs of compounds with carboxyl functional groups are the lower alkyl esters of the carboxylic acid.
  • the carboxylate esters are conveniently formed by esterifying any of the carboxylic acid moieties present on the molecule.
  • Prodrugs can typically be prepared using well-known methods, such as those described by Burger 's Medicinal Chemistry and Drug Discovery 6 th ed. (Donald J.
  • stereomerically pure means one stereoisomer of a TOR kinase inhibitor that is substantially free of other stereoisomers of that compound.
  • a stereomerically pure compound having one chiral center will be substantially free of the opposite enantiomer of the compound.
  • a stereomerically pure compound having two chiral centers will be substantially free of other diastereomers of the compound.
  • a typical stereomerically pure compound comprises greater than about 80% by weight of one stereoisomer of the compound and less than about 20% by weight of other stereoisomers of the compound, greater than about 90% by weight of one stereoisomer of the compound and less than about 10%> by weight of the other stereoisomers of the compound, greater than about 95% by weight of one stereoisomer of the compound and less than about 5% by weight of the other stereoisomers of the compound, or greater than about 97% by weight of one stereoisomer of the compound and less than about 3% by weight of the other stereoisomers of the compound.
  • the TOR kinase inhibitors can have chiral centers and can occur as racemates, individual enantiomers or diastereomers, and mixtures thereof.
  • the TOR kinase inhibitors can include E and Z isomers, or a mixture thereof, and cis and trans isomers or a mixture thereof.
  • the TOR kinase inhibitors are isolated as either the cis or trans isomer. In other embodiments, the TOR kinase inhibitors are a mixture of the cis and trans isomers.
  • Tautomers refers to isomeric forms of a compound that are in equilibrium with each other. The concentrations of the isomeric forms will depend on the environment the compound is found in and may be different depending upon, for example, whether the compound is a solid or is in an organic or aqueous solution. For example, in aqueous solution, pyrazoles may exhibit the following isomeric forms, which are referred to as tautomers of each other: [0087] As readily understood by one skilled in the art, a wide variety of functional groups and other stuctures may exhibit tautomerism and all tautomers of the TOR kinase inhibitors are within the scope of the present invention.
  • TOR kinase inhibitors can contain unnatural
  • the compounds may be radiolabeled with radioactive isotopes, such as for example tritium ( 3 H), iodine- 125 ( 125 I), sulfur-35 ( 35 S), or carbon-14 ( 14 C), or may be isotopically enriched, such as with deuterium ( 2 H), carbon- 13 ( 13 C), or nitrogen- 15 ( 15 N).
  • an "isotopologue” is an isotopically enriched compound.
  • the term “isotopically enriched” refers to an atom having an isotopic composition other than the natural isotopic composition of that atom.
  • isotopically enriched may also refer to a compound containing at least one atom having an isotopic composition other than the natural isotopic composition of that atom.
  • isotopic composition refers to the amount of each isotope present for a given atom.
  • Radiolabeled and isotopically encriched compounds are useful as therapeutic agents, e.g., cancer and inflammation therapeutic agents, research reagents, e.g., binding assay reagents, and diagnostic agents, e.g., in vivo imaging agents. All isotopic variations of the TOR kinase inhibitors as described herein, whether radioactive or not, are intended to be encompassed within the scope of the embodiments provided herein.
  • isotopologues of the TOR kinase inhibitors for example, the isotopologues are deuterium, carbon- 13, or nitrogen- 15 enriched TOR kinase inhibitors.
  • Treating means an alleviation, in whole or in part, of symptoms associated with a disorder or disease (e.g., cancer or a tumor syndrome), or slowing, or halting of further progression or worsening of those symptoms.
  • a disorder or disease e.g., cancer or a tumor syndrome
  • Preventing means the prevention of the onset, recurrence or spread, in whole or in part, of the disease or disorder (e.g. , cancer), or a symptom thereof.
  • the term "effective amount" in connection with an TOR kinase means an amount alone or in combination capable of alleviating, in whole or in part, a symptom associated with a cancer, or slowing or halting further progression or worsening of those symptoms, or treating or preventing a cancer in a subject having or at risk for having a cancer.
  • the effective amount of the TOR kinase inhibitor for example in a pharmaceutical composition, may be at a level that will exercise the desired effect; for example, about 0.005 mg/kg of a subject's body weight to about 100 mg/kg of a patient's body weight in unit dosage for both oral and parenteral administration.
  • carcinomas Malignancies of epithelial glandular tissue such as are found in the breast, prostate, and colon, are known as adenocarcinomas.
  • Lymphomas and leukemias are malignancies arising among white blood cells.
  • Bone tissues are one of the most favored sites of metastases of malignant tumors, occurring in about 30% of all cancer cases.
  • cancers of the lung, breast, prostate or the like are particularly known to be likely to metastasize to bone.
  • prevention or chemoprevention includes either preventing the onset of clinically evident neoplasia altogether or preventing the onset of a preclinically evident stage of neoplasia in individuals at risk. Also intended to be encompassed by this definition is the prevention of transformation into malignant cells or to arrest or reverse the progression of premalignant cells to malignant cells. This includes prophylactic treatment of those at risk of developing the neoplasia.
  • wild type refers to the typical or most common form of a characteristic (for example, gene sequence or presence, or protein sequence, presence, level or activity), as it occurs in nature, and the reference against which all others are compared.
  • wild type refers to the typical gene sequence(s) or gene expression levels as they most commonly occur in nature.
  • a "control patient”, as used herein is a patient who exhibits the wild type gene sequence(s) or gene or protein expression levels.
  • the gene sequence is the gene sequence of one or more of the genes set forth in Table 1, i.e, PIK3CA, RICTOR, TP53, IGFIR and/or PTEN.
  • the gene sequence is the gene sequence of one or more of RICTOR, TP53 or IGFIR. In some such embodiments, a further gene sequence is PIK3CA. In one embodiment, the gene sequence is the gene sequence of AKTl . In one embodiment, the gene sequence is the gene sequence of AKT2. In certain embodiments, the gene sequence is the gene sequence of one or more of the genes set forth in FIG. 2. In another embodiment, the gene sequence is the gene sequence of one or more of genes set forth in Table 2 or Table 3. In yet another, the gene sequence is the gene sequence of one or more genes set forth in Table 4.
  • tumor samples are collected and DNA is extracted from tumor samples (for example, pre-treatment tumor samples) and submitted for next generation sequencing (for example at Foundation Medicine, Inc (FMI)).
  • FMI Foundation Medicine, Inc
  • a gene is considered to be mutant (variant) if it shows one of the following: mutation(s) (likely or known somatic variants, or variants of unknown significance), or structural variation (deletion, amplification or
  • a gene is considered to be wild type when no sequencing alterations (variants) are detected for this gene.
  • a gene cluster is considered to be mutated if any gene in the cluster is mutated as defined above; otherwise the gene cluster is considered to be wild type.
  • gene mutation indicates a deviation from wild type or non-mutated state. These include single or multiple base changes, nucleotide insertions or nucleotide deletions (single or multiple bases in either case), copy number changes including loss of one copy or focal or large amplifications of segments of DNA, or
  • gene mutation refers to a gene mutation resulting in, for example, an increase or a decrease in mRNA expression, an increase or decrease in protein production, a non-functional protein or a protein with altered function, as compared to wild type.
  • gene or protein loss refers to a reduced level of gene or protein or the absence of gene or protein, as compared to wild type levels.
  • expression refers to the transcription from a gene to give an R A nucleic acid molecule complementary at least in part to a region of one of the two nucleic acid strands of the gene.
  • expression also refers to the translation from the RNA molecule to give a protein, a polypeptide or a portion thereof.
  • the expression of a gene that is "upregulated” is generally “increased” relative to wild type.
  • the expression of a gene that is “downregulated” is generally “decreased” relative to wild type.
  • a gene from a patient sample can be "upregulated,” i.e., gene expression can be increased, for example, by about 5%, 10%, 20%>, 30%>, 40%>, 50%>, 60%>, 70%>, 90%, 100%, 200%, 300%, 500%, 1,000%, 5,000% or more of a comparative control, such as wild type.
  • a gene from a patient sample can be "downregulated," i.e., gene expression can be decreased, for example, by about 99%, 95%, 90%, 80%, 70%, 60%, 50%, 40%, 30%), 20%), 10%), 1%) or less of a comparative control, such as wild type.
  • reduced level or “loss” means a reduction in level relative to levels observed in wild type. In one embodiment the reduction is 10%> - 50%> or 50%>-100%>. In some embodiments, the reduction is 20%, 30%, 40%, 50%, 60%, 70%, 80%. 90% or 100% (complete loss) relative to wild type.
  • patient and “subject” as used herein include an animal, including, but not limited to, an animal such as a cow, monkey, horse, sheep, pig, chicken, turkey, quail, cat, dog, mouse, rat, rabbit or guinea pig, in one embodiment a mammal, in another embodiment a human.
  • an animal such as a cow, monkey, horse, sheep, pig, chicken, turkey, quail, cat, dog, mouse, rat, rabbit or guinea pig, in one embodiment a mammal, in another embodiment a human.
  • a "patient” or “subject” is a human whose DNA comprises a gene mutation or variant, relative to that of a control patient or wild type.
  • a "patient” or “subject” is a human whose DNA contains a gene mutation or variant, relative to that of a control patient or wild type.
  • a "patient” or “subject” is a human having a gene mutation or variant, relative to that of a control patient or wild type.
  • a "patient” or “subject” is a human having a gene mutation or variant, relative to that of a control patient or wild type, and also having a cancer characterized by a gene mutation or variant, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • the gene mutation or variant is identified by certain gene sequence(s), determined using, for example, Sanger sequencing, di-deoxy chain termination sequencing, massively parallel next generation sequencing (NGS), or PCR based methods and compared to wild type, using analytical pipelines that process raw sequence data for tumor samples and reference samples, filter out data artifacts from the sequencing process; filter out known polymorphisms and identify the mutation variants present in the tumor sample (see J.
  • the mutation is in one or more of the genes set forth in Table 1, i.e. PIK3CA, RICTOR, TP53, IGF1R and/or PTEN. In one embodiment, the mutation is in one or more of RICTOR, TP53 or IGF1R. In some such embodiments, a further mutation is a mutation in PIK3CA. In one embodiment, the mutation is a mutation in the gene sequence of AKT1. In one embodiment, the mutation is a gene amplication mutation in the gene sequence of AKT2. In certain embodiments, the variant is in one or more of the genes set forth in Fig. 2.
  • the variant is in one or more of the genes set forth in Table 2 or Table 3. In certain embodiments, the variant is in one or more of the genes set forth in Table 4. In one embodiment, the variant is one or more known somatic-variants, likely-somatic variants, rearrangements, variants-of-unknown-significance, or copy-number variants, for example, amplifications or deletions, or a combination thereof. In one embodiment, the variant is one or more known somatic variants. In another embodiment, the variant is one or more likely somatic- variants. In one embodiment, the variant is one or more rearrangements. In one embodiment, the variant is one or more variants-of-unknown-significance. In one embodiment, the variant is one or more amplifications. In another embodiment, the variant is one or more deletions.
  • predict generally means to determine or tell in advance.
  • predict the effectiveness of a cancer
  • the term “predict” can mean that the likelihood of the outcome of the treatment can be determined at the outset, before the treatment has begun, or before the treatment period has progressed substantially.
  • determining generally refer to any form of measurement, and include determining if an element is present or not. These terms include both quantitative and/or qualitative determinations.
  • inhibition may be assessed by inhibition of disease progression, inhibition of tumor growth, reduction of primary tumor, relief of tumor-related symptoms, inhibition of tumor secreted factors (including tumor secreted hormones, such as those that contribute to carcinoid syndrome), delayed appearance of primary or secondary tumors, slowed development of primary or secondary tumors, decreased occurrence of primary or secondary tumors, slowed or decreased severity of secondary effects of disease, arrested tumor growth and regression of tumors, increased Time To Progression (TTP), increased Progression Free Survival (PFS), increased Overall Survival (OS), among others.
  • OS as used herein means the time from randomization (for example, first dose date) until death from any cause, and is measured in the intent-to-treat population.
  • TTP as used herein means the time from
  • prevention or chemoprevention includes either preventing the onset of clinically evident advanced cancer altogether or preventing the onset of a
  • preclinically evident stage of a cancer Also intended to be encompassed by this definition is the prevention of transformation into malignant cells or to arrest or reverse the progression of premalignant cells to malignant cells. This includes prophylactic treatment of those at risk of developing a cancer.
  • the treatment of a cancer may be assessed by Response
  • CR complete response
  • PR partial response
  • SD stable disease
  • PD progressive disease.
  • complete response is the disappearance of all target lesions
  • partial response is at least a 30% decrease in the sum of the longest diameter of target lesions, taking as reference the baseline sum longest diameter
  • progressive disease is at least a 20% increase in the sum of the longest diameter of target lesions, taking as reference the smallest sum longest diameter recorded since the treatment started or the appearance of one or more new lesions
  • stable disease is neither sufficient shrinkage to qualify for partial response nor sufficient increase to qualify for progressive disease, taking as reference the smallest sum longest diameter since the treatment started.
  • complete response is the disappearance of all non-target lesions and normalization of tumor marker level
  • incomplete response/stable disease is the persistence of one or more non-target lesion(s) and/or the maintenance of tumor marker level above the normal limits
  • progressive disease is the appearance of one or more new lesions and/or unequivocal progression of existing non-target lesions.
  • the treatment of lymphoma may be assessed by the
  • CR complete remission
  • FDG [ 18 F]fluorodeoxyglucose
  • PET positron emission tomography
  • CT computed tomography
  • PR partial remission
  • SPD sum of the product of the diameters
  • SD stable disease
  • PD progressive disease.
  • CR complete remission
  • PR partial remission
  • Clinical benefit may reflect improvement in quality of life, or reduction in patient symptoms, transfusion requirements, frequent infections, or other parameters. Time to reappearance or progression of lymphoma-related symptoms can also be used in this end point.
  • the treatment of CLL may be assessed by the International
  • Group A criteria define the tumor load
  • Group B criteria define the function of the hematopoietic system (or marrow).
  • CR complete remission
  • PR partial remission
  • SD absence of progressive disease (PD) and failure to achieve at least a PR
  • PD at least one of the above criteria of group A or group B has to be met.
  • the treatment of multiple myeloma may be assessed by the
  • IURC International Uniform Response Criteria for Multiple Myeloma
  • CR complete response
  • FLC free light chain
  • PR partial response
  • cPresence/absence of clonal cells is based upon the ⁇ / ⁇ ratio.
  • immunohistochemistry and/or immunofluorescence requires a minimum of 100 plasma cells for analysis.
  • An abnormal ratio reflecting presence of an abnormal clone is ⁇ / ⁇ of >4: 1 or
  • d Measurable disease defined by at least one of the following measurements: Bone marrow plasma cells >30%; Serum M-protein >1 g/dl (>10 gm/l)[10 g/1]; Urine M-protein >200 mg/24 h; Serum FLC assay: Involved FLC level >10 mg/dl (>100 mg/1); provided serum FLC ratio is abnormal.
  • the baseline MRI scan is defined as the assessment performed at the end of the post-surgery rest period, prior to re-initiating compound treatment.
  • the baseline MRI is used as the reference for assessing complete response (CR) and partial response (PR).
  • CR complete response
  • PR partial response
  • the smallest SPD sum of the products of perpendicular diameters obtained either at baseline or at subsequent assessments will be designated the nadir assessment and utilized as the reference for determining progression.
  • subjects receive either no
  • glucocorticoids or are on a stable dose of glucocorticoids.
  • a stable dose is defined as the same daily dose for the 5 consecutive days preceding the MRI scan. If the prescribed glucocorticoid dose is changed in the 5 days before the baseline scan, a new baseline scan is required with glucocorticoid use meeting the criteria described above. The following definitions will be used.
  • Measurable lesions are contrast-enhancing lesions that can be measured bidimensionally. A measurement is made of the maximal enhancing tumor diameter (also known as the longest diameter, LD). The greatest perpendicular diameter is measured on the same image. The cross hairs of bidimensional measurements should cross and the product of these diameters will be calculated.
  • Minimal Diameter Tl -weighted image in which the sections are 5 mm with 1 mm skip.
  • the minimal LD of a measurable lesion is set as 5 mm by 5 mm. Larger diameters may be required for inclusion and/or designation as target lesions. After baseline, target lesions that become smaller than the minimum requirement for measurement or become no longer amenable to bidimensional measurement will be recorded at the default value of 5 mm for each diameter below 5 mm. Lesions that disappear will be recorded as 0 mm by 0 mm.
  • Multicentric Lesions Lesions that are considered multicentric (as opposed to continuous) are lesions where there is normal intervening brain tissue between the two (or more) lesions. For multicentric lesions that are discrete foci of enhancement, the approach is to separately measure each enhancing lesion that meets the inclusion criteria. If there is no normal brain tissue between two (or more) lesions, they will be considered the same lesion.
  • Nonmeasurable Lesions All lesions that do not meet the criteria for measurable disease as defined above will be considered non-measurable lesions, as well as all nonenhancing and other truly nonmeasurable lesions. Nonmeasurable lesions include foci of enhancement that are less than the specified smallest diameter (i.e., less than 5 mm by 5 mm), nonenhancing lesions
  • FLAIR FLAIR images
  • Hemorrhagic lesions often have intrinsic Tl -weighted hyperintensity that could be misinterpreted as enhancing tumor, and for this reason, the pre-contrast Tl -weighted image may be examined to exclude baseline or interval sub-acute hemorrhage.
  • 5 measurable lesions can be selected as target lesions with each measuring at least 10 mm by 5 mm, representative of the subject's disease;
  • Non-target lesions All other lesions, including all nonmeasurable lesions (including mass effects and T2/FLAIR findings) and any measurable lesion not selected as a target lesion.
  • target lesions are to be measured as described in the definition for measurable lesions and the SPD of all target lesions is to be determined. The presence of all other lesions is to be documented.
  • the baseline classification of lesions as target and non-target lesions will be maintained and lesions will be documented and described in a consistent fashion over time (e.g. , recorded in the same order on source documents and eCRFs).
  • All measurable and nonmeasurable lesions must be assessed using the same technique as at baseline (e.g., subjects should be imaged on the same MRI scanner or at least with the same magnet strength) for the duration of the study to reduce difficulties in interpreting changes.
  • target lesions will be measured and the SPD calculated.
  • Non-target lesions will be assessed qualitatively and new lesions, if any, will be documented separately.
  • a time point response will be determined for target lesions, non- target lesions, and new lesion. Tumor progression can be established even if only a subset of lesions is assessed. However, unless progression is observed, objective status (stable disease, PR or CR) can only be determined when all lesions are assessed.
  • treatment of a cancer may be assessed by the inhibition of phosphorylation of S6RP, 4E-BP1 , AKT and/or DNA-PK in circulating blood and/or tumor cells, and/or skin biopsies or tumor biopsies/aspirates, before, during and/or after treatment with a TOR kinase inhibitor.
  • the inhibition of phosphorylation of S6RP, 4E-BP1 , AKT and/or DNA-PK is assessed in B-cells, T-cells and/or monocytes.
  • treatment of a cancer may be assessed by the inhibition of DNA-dependent protein kinase (DNA-PK) activity in skin samples and/or tumor biopsies/aspirates, such as by assessment of the amount of pDNA-PK S2056 as a biomarker for DNA damage pathways, before, during, and/or after TOR kinase inhibitor treatment.
  • the skin sample is irradiated by UV light.
  • prevention or chemoprevention includes either preventing the onset of clinically evident cancer altogether or preventing the onset of a preclinically evident stage of a cancer.
  • TOR kinase inhibitor(s) do not include rapamycin or rapamycin analogs (rapalogs).
  • the TOR kinase inhibitors include compounds having the following formula (I):
  • R 1 is substituted or unsubstituted Ci_g alkyl, substituted or unsubstituted aryl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl, or substituted or unsubstituted heterocyclylalkyl;
  • R 2 is H, substituted or unsubstituted Ci_ 8 alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted
  • heterocyclylalkyl substituted or unsubstituted aralkyl, or substituted or unsubstituted
  • R 3 is H, or a substituted or unsubstituted Ci_g alkyl
  • the TOR kinase inhibitors do not include 7-(4- hydroxyphenyl)- 1 -(3 -methoxybenzyl)-3 ,4-dihydropyrazino [2,3 -b]pyrazin-2( 1 H)-one, depicted below:
  • R 1 is substituted or unsubstituted aryl or substituted or unsubstituted heteroaryl.
  • R 1 is phenyl, pyridyl, pyrimidyl, benzimidazolyl, lH-pyrrolo[2,3-b]pyridyl, indazolyl, indolyl, lH-imidazo[4,5- b]pyridyl, lH-imidazo[4,5-b]pyridin-2(3H)-onyl, 3H-imidazo[4,5-b]pyridyl, or pyrazolyl, each optionally substituted.
  • R 1 is phenyl substituted with one or more substituents independently selected from the group consisting of substituted or unsubstituted Ci_8 alkyl (for example, methyl), substituted or unsubstituted heterocyclyl (for example, a substituted or unsubstituted triazolyl or pyrazolyl), aminocarbonyl, halogen (for example, fluorine), cyano, hydroxyalkyl and hydroxy.
  • substituents independently selected from the group consisting of substituted or unsubstituted Ci_8 alkyl (for example, methyl), substituted or unsubstituted heterocyclyl (for example, a substituted or unsubstituted triazolyl or pyrazolyl), aminocarbonyl, halogen (for example, fluorine), cyano, hydroxyalkyl and hydroxy.
  • R 1 is pyridyl substituted with one or more substituents independently selected from the group consisting of substituted or unsubstituted Ci_ 8 alkyl (for example, methyl), substituted or unsubstituted heterocyclyl (for example, a substituted or unsubstituted triazolyl), halogen, aminocarbonyl , cyano, hydroxyalkyl (for example, hydroxypropyl), -OR, and -NR 2 , wherein each R is independently H, or a substituted or unsubstituted Ci_ 4 alkyl.
  • substituents independently selected from the group consisting of substituted or unsubstituted Ci_ 8 alkyl (for example, methyl), substituted or unsubstituted heterocyclyl (for example, a substituted or unsubstituted triazolyl), halogen, aminocarbonyl , cyano, hydroxyalkyl (for example, hydroxypropyl), -OR, and -NR 2
  • R 1 is lH-pyrrolo[2,3-b]pyridyl or benzimidazolyl, optionally substituted with one or more substituents independently selected from the group consisting of substituted or unsubstituted Ci_g alkyl, and -NR 2 , wherein R is independently H, or a substituted or unsubstituted Ci_ 4 alkyl. [00128] In some embodiments, R 1 is
  • R is at each occurrence independently H, or a substituted or unsubstituted Ci_4 alkyl (for example, methyl); R' is at each occurrence independently a substituted or unsubstituted Ci_ 4 alkyl (for example, methyl), halogen (for example, fluoro), cyano, -OR, or - NR 2 ; m is 0-3; and n is 0-3. It will be understood by those skilled in the art that any of the subsitutuents R' may be attached to any suitable atom of any of the rings in the fused ring systems.
  • R is at each occurrence independently H, or a substituted or unsubstituted
  • Ci_4 alkyl is at each occurrence independently a substituted or unsubstituted Ci_ 4 alkyl, halogen, cyano, -OR or -NR 2 ; m is 0-3; and n is 0-3.
  • R 2 is H, substituted or unsubstituted Ci_ 8 alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted Ci_ 4 alkyl-heterocyclyl, substituted or unsubstituted Ci_ 4 alkyl-aryl, or substituted or unsubstituted Ci_ 4 alkyl-cycloalkyl.
  • R 2 is H, methyl, ethyl, n-propyl, isopropyl, n-butyl, sec-butyl, isobutyl, tert-butyl, n-pentyl, isopentyl, cyclopentyl, cyclohexyl, tetrahydrofuranyl, tetrahydropyranyl, (C 1-4 alkyl)-phenyl, (C 1-4 alkyl)-cyclopropyl, (Ci_ 4 alkyl)-cyclobutyl, (C 1-4 alkyl)-cyclopentyl, (C 1-4 alkyl)-cyclohexyl, (C 1-4 alkyl)-pyrrolidyl, (Ci_ 4 alkyl)-piperidyl, (C 1-4 alkyl)-piperazinyl, (C 1-4 alkyl)-morpholinyl,
  • R is at each occurrence independently H, or a substituted or unsubstituted Ci_ 4 alkyl (for example, methyl); R' is at each occurrence independently H, -OR, cyano,or a substituted or unsubstituted Ci_ 4 alkyl (for example, methyl); and p is 0-3.
  • R 2 is H, Ci_ 4 alkyl
  • R is at each occurrence independently H, or a substituted or unsubstituted Ci_2 alkyl
  • R' is at each occurrence independently H, -OR, cyano, or a substituted or unsubstituted Ci_2 alkyl
  • p is 0-1.
  • R 3 is H.
  • R 1 is substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
  • R 1 is phenyl, pyridyl, pyrimidyl, benzimidazolyl, lH-pyrrolo[2,3-b]pyridyl, indazolyl, indolyl, lH-imidazo[4,5-b]pyridine, pyridyl, lH-imidazo[4,5-b]pyridin-2(3H)-onyl, 3H-imidazo[4,5-b]pyridyl, or pyrazolyl, each optionally substituted.
  • R 1 is phenyl substituted with one or more substituents independently selected from the group consisting of substituted or unsubstituted Ci_8 alkyl, substituted or unsubstituted heterocyclyl, aminocarbonyl, halogen, cyano,
  • R 1 is pyridyl substituted with one or more substituents independently selected from the group consisting of Ci_g alkyl, substituted or unsubstituted heterocyclyl, halogen, aminocarbonyl, cyano, hydroxyalkyl, -OR, and -NR 2 , wherein each R is independently H, or a substituted or unsubstituted Ci_ 4 alkyl.
  • R 1 is lH-pyrrolo[2,3- b]pyridyl or benzimidazolyl, optionally substituted with one or more substituents independently selected from the group consisting of substituted or unsubstituted Ci_g alkyl, and -NR 2 , wherein R is independently H, or a substituted or unsubstituted Ci_ 4 alkyl.
  • R 1 is pyridyl substituted with one or more substituents independently selected from the group consisting of Ci_ 8 alkyl, substituted or unsubstituted heterocyclyl, halogen, aminocarbonyl, cyano, hydroxyalkyl, -OR, and -NR 2 , wherein each R is independently H, or a substituted or unsubstituted Ci_ 4 alkyl, and R 2 is H, substituted or unsubstituted Ci_g alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocyclyl, substituted or unsubstituted Ci_ 4 alkyl-heterocyclyl, substituted or unsubstituted Ci_ 4 alkyl-aryl, or substituted or unsubstituted Ci_ 4 alkyl-cycloalkyl.
  • R 1 is pyridyl substituted with one or more substituents independently selected from the group consisting of Ci_g alkyl, substituted or unsubstituted heterocyclyl, or hydroxyalkyl
  • R 2 is substituted or unsubstituted Ci_ 8 alkyl, or substituted or unsubstituted cycloalkyl.
  • the compounds of formula (I) have an R 1 group set forth herein and an R 2 group set forth herein.
  • the compound at a concentration of 10 ⁇ inhibits mTOR, DNA-PK, PI3K, or a combination thereof by at least about 50%.
  • Compounds of formula (I) may be shown to be inhibitors of the kinases above in any suitable assay system.
  • Representative TOR kinase inhibitors of formula (I) include compounds from
  • the TOR kinase inhibitor is a Compound 1 , Compound 2,
  • the TOR kinase inhibitor is Compound 1 (a TOR kinase inhibitor set forth herein having molecular formula C 21 H 27 N 5 O 3 ). In one
  • the TOR kinase inhibitor is Compound 2 (a TOR kinase inhibitor set forth herein having molecular formula C ⁇ H ⁇ NeO). In one embodiment, the TOR kinase inhibitor is
  • Compound 3 (a TOR kinase inhibitor set forth herein having molecular formula C 21 H 24 N 8 O 2 ).
  • the TOR kinase inhibitor is Compound 4 (a TOR kinase inhibitor set forth herein having molecular formula C 20 H 25 N 5 O 3 ).
  • Compound 1 is 7-(6-(2- hydroxypropan-2-yl)pyridin-3 -yl)- 1 -((trans)-4-methoxycyclohexyl)-3 ,4-dihydropyrazino [2,3 - 3 ⁇ 4]pyrazin-2(lH)-one, also having the chemical names 7-(6-(2-hydroxypropan-2-yl)pyridin-3-yl)- l-((lr,4r)-4-methoxycyclohexyl)-3,4-dihydropyrazino[2,3-b]pyrazin-2(lH)-one and 7-(6-(2- hydroxypropan-2-yl)pyridin-3 -yl)- 1 -(( 1 R* ,4R*)-4-methoxy eye lohexyl)-3 ,4-dihydropyrazino [2,3 - b]pyrazin-2(lH)-one, which has the following
  • Compound 2 is l-ethyl-7-(2-methyl-6-(lH-l ,2,4-triazol-3- yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3-b]pyrazin-2(lH)-one or a tautomer thereof, for example, l-ethyl-7-(2-methyl-6-(4H-l ,2,4-triazol-3-yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3-b]pyrazin- 2( 1 H)-one, or 1 -ethyl-7-(2-methyl-6-( 1 H- 1 ,2,4-triazol-5 -yl)pyridin-3 -yl)-3 ,4- dihydropyrazino[2,3-b]pyrazin-2(lH)-one.
  • Compound 3 is 7-(2-methyl- 6-(4H-l ,2,4-triazol-3-yl)pyridin-3-yl)-l-(2-(tetrahydro-2H-pyran-4-yl)ethyl)-3,4- dihydropyrazino[2,3-b]pyrazin-2(lH)-one.
  • Compound 4 is l-((tra/?5)-4- hydroxycyclohexyl)-7-(6-(2-hydroxypropan-2-yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3- b]pyrazin-2(lH)-one, alternatively named l-((lr,4r)-4-hydroxycyclohexyl)-7-(6-(2- hydroxypropan-2-yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3-b]pyrazin-2(lH)-one.
  • Compound 4 is a metabolite of Compound 1.
  • the TOR kinase inhibitors can be obtained via standard, well-known synthetic methodology, see e.g. , March, J. Advanced Organic Chemistry; Reactions Mechanisms, and Structure, 4th ed., 1992. Starting materials useful for preparing compounds of formula (III) and intermediates therefore, are commercially available or can be prepared from commercially available materials using known synthetic methods and reagents.
  • a cancer characterized by a gene mutation for example, breast cancer
  • administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a particular gene mutation, relative to wild type comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a particular gene mutation, relative to wild type.
  • the gene mutation occurs in one or more genes from Table 1 , i.e. PIK3CA, RICTOR, TP53, IGFIR or PTEN.
  • the mutation is a mutation in one or more of RICTOR, TP53 or IGFIR.
  • a further mutation is a mutation in PIK3CA.
  • the mutation is a mutation in the gene sequence of AKTl .
  • the mutation is a gene amplication mutation in the gene sequence of AKT2.
  • the mutation is a mutation in RICTOR.
  • the mutation is a mutation in TP53.
  • the mutation is a mutation in IGFIR.
  • a further mutation results in PTEN loss.
  • the breast cancer is ER+. In some such embodiments, the breast cancer is PR+. In other embodiments, the breast cancer is
  • ER+/PR+ Provided herein are also the TOR kinase inhibitors of the present invention for use in methods described herein.
  • the gene mutation is a single base change. In another, the gene mutation is a multiple base change. In yet another, the gene mutation is one or more nucleotide insertions. In still another, the gene mutation is one or more nucleotide deletions. In some embodiments, the gene mutation is a copy number change, including loss of one copy or focal or large amplifications of segments of DNA. In yet another embodiment, the gene mutation is a rearrangement of the DNA, wherein the DNA strands break and are rejoined differently from the wild type.
  • a cancer characterized by a gene mutation for example breast cancer
  • methods for treating or preventing a cancer characterized by a gene mutation comprising screening a patient's cancer for the presence of a particular gene mutation relative to wild type, and administering an effective amount of a TOR kinase inhibitor to the patient having a cancer characterized by a particular gene mutation.
  • TOR kinase inhibitor in a patient having a cancer characterized by a gene mutation, for example breast cancer comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of one or more genes selected from Table 1 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of a mutation indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • a TOR kinase inhibitor treatment of a patient having a cancer characterized by a gene mutation, for example breast cancer with a TOR kinase inhibitor
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence(s) of one or more genes selected from Table 1 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of a mutation indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • a breast cancer characterized by a gene mutation comprising administering an effective amount of a TOR kinase inhibitor to a patient having a breast cancer characterized by a gene mutation, relative to wild type, wherein the gene mutation is a mutation in the gene sequence of AKT1 or a gene amplication mutation in the gene sequence of AKT2.
  • a breast cancer characterized by a gene mutation comprising screening a patient's breast cancer for the presence of a gene mutation relative to wild type, and administering an effective amount of a TOR kinase inhibitor to the patient having a cancer characterized by a gene mutation, wherein the gene mutation is a mutation in the gene sequence of AKT1 or a gene amplication mutation in the gene sequence of AKT2.
  • TOR kinase inhibitor in a patient having a breast cancer characterized by a gene mutation comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of a gene selected from AKT1 and AKT2 in said biological test sample; c) comparing said gene sequence to the gene sequence of a biological wild-type sample; wherein the presence of a mutation in the gene sequence of AKT1 or the presence of a gene amplification mutation in the gene sequence of AKT2 indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • TOR kinase inhibitor treatment of a patient having a breast cancer characterized by a gene mutation, with a TOR kinase inhibitor
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of a gene selected from AKT1 and AKT2 in said biological test sample; c) comparing said gene sequence to the gene sequence of a biological wild-type sample; wherein the presence of a mutation in the gene sequence of AKT1 or the presence of a gene amplification mutation in the gene sequence of AKT2 indicates indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • the gene sequence(s) of the biological test sample is obtained using, for example, Sanger sequencing, di-deoxy chain termination sequencing, massively parallel next generation sequencing (NGS), or PCR based methods.
  • NGS massively parallel next generation sequencing
  • comparison of gene sequences is performed using analytical pipelines that process raw sequence data for tumor samples and reference samples, filter out data artifacts from the sequencing process; filter out known polymorphisms and identify the mutation variants present in the tumor sample.
  • the gene mutation or loss results in a decrease in mRNA expression (e.g., relative to wild type). In another embodiment, the gene mutation or loss results in a change in mRNA structure (e.g., relative to wild type). In another embodiment, the gene mutation results in a decrease in protein production (e.g., relative to wild type). In another embodiment, the gene mutation results in a change in protein structure (e.g., relative to wild type).
  • Types of gene mutations contemplated include mutations of the DNA sequence in which the number of bases is altered, categorized as insertion or deletion mutations (including frameshift mutations and full gene deletions), and mutations of the DNA that change one base into another, categorized as missense mutations, which are subdivided into the classes of transitions (one purine to another purine, or one pyrimidine to another pyrimidine) and transversions (a purine to a pyrimidine, or a pyrimidine to a purine) and nonsense mutations, wherein a codon encoding an amino acid is changed to a stop codon, thus resulting in truncated protein.
  • mutations comtemplated include copy number alterations wherein one full copy of the gene may be lost (loss of heterozygosity or LOH) or the entire gene may be replicated resulting in an amplified number of gene copies (gene amplification); similarly translocatons where the double strand of DNA is broken and rejoined with a new segment of DNA may result in an altered, truncated or over expressed transcript and protein.
  • the gene mutation(s), for example, in a biological test sample, as referenced herein is present in the sequence(s) of one or more of the genes set forth in Table 1, i.e. in one or more of PIK3CA, RICTOR, TP53, IGFIR and PTEN.
  • the gene mutation is a mutation in one or more of RICTOR, TP53 or IF1G1.
  • the gene mutation is a mutation in one or more of RICTOR, TP53 or IGFIR in addition to one or more of the genes set forth in Table 1.
  • a further gene mutation is a mutation in PIK3CA.
  • the mutation is a mutation in the gene sequence of AKT1.
  • the mutation is a gene amplication mutation in the gene sequence of AKT2.
  • the gene mutation is a somatic mutation.
  • a cancer characterized by one or more gene variants for example, breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by one or more particular gene variants, relative to wild type.
  • gene variants occur in one or more genes from Fig. 2. In some embodiments described herein, gene variants occur in one or more genes from Table 2 or Table 3. In some embodiments, the gene variants occur in one or more genes of patients showing a best overall response of Stable Disease (SD), Partial Response (PR) or Non- Progression.
  • SD Stable Disease
  • PR Partial Response
  • the variant is one or more known somatic- variants, likely- somatic variants, rearrangements, variants-of-unknown-significance, or copy-number variants, for example, amplifications or deletions, or a combination thereof.
  • the variant is one or more known somatic variants.
  • the variant is one or more likely somatic- variants.
  • the variant is one or more rearrangements.
  • the variant is one or more variants-of-unknown- significance.
  • the variant is one or more amplifications.
  • the variant is one or more deletions.
  • a cancer characterized by one or more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, comprising screening a patient's cancer for the presence of one or more particular gene variants relative to wild type, for example in one or more genes from FIG. 2, and administering an effective amount of a TOR kinase inhibitor to the patient having a cancer characterized by one or more particular gene variants.
  • TOR kinase inhibitor in a patient having a cancer characterized by one or more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of the genes listed in Fig. 2 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants in one or more genes selected from Fig. 2, Table 2 or Table 3 indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • TOR kinase inhibitor in a patient having a cancer characterized by one or more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence of one or more genes selected from Table 2 or Table 3 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence(s) of the genes listed in Fig. 2 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants of one or more genes selected from Fig. 2, Table 2 or Table 3 indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • TOR kinase inhibitor treatment of a patient having a cancer characterized by one ore more gene variants for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, with a TOR kinase inhibitor
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the gene sequence(s) of one or more genes selected from Table 2 or Table 3 in said biological test sample; c) comparing said gene sequence(s) to the gene sequence(s) of a biological wild-type sample; wherein the presence of one or more variants indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • the gene sequence(s) of the biological test sample is obtained using, for example, Sanger sequencing, di-deoxy chain termination sequencing, massively parallel next generation sequencing (NGS), or PCR based methods.
  • NGS massively parallel next generation sequencing
  • comparison of gene sequences is performed using analytical pipelines that process raw sequence data for tumor samples and reference samples, filter out data artifacts from the sequencing process; filter out known polymorphisms and identify the variants present in the tumor sample.
  • the gene variant results in a decrease in mRNA expression
  • the gene variant results in a change in mR A structure (e.g., relative to wild type). In another embodiment, the gene variant results in a decrease in protein production (e.g., relative to wild type). In another embodiment, the gene variant results in a change in protein structure (e.g., relative to wild type).
  • Types of gene variants contemplated include mutations of the DNA sequence in which the number of bases is altered, categorized as insertion or deletion mutations (including frameshift mutations and full gene deletions), and mutations of the DNA that change one base into another, categorized as missense mutations, which are subdivided into the classes of transitions (one purine to another purine, or one pyrimidine to another pyrimidine) and transversions (a purine to a pyrimidine, or a pyrimidine to a purine) and nonsense mutations, wherein a codon encoding an amino acid is changed to a stop codon, thus resulting in truncated protein.
  • variants comtemplated include copy number alterations wherein one full copy of the gene may be lost (loss of heterozygosity or LOH) or the entire gene may be replicated resulting in an amplified number of gene copies (gene amplification); similarly translocatons where the double strand of DNA is broken and rejoined with a new segment of DNA may result in an altered, truncated or over expressed transcript and protein.
  • the gene variant(s), for example, in a biological test sample, as referenced herein, is present in the sequence(s) of one or more of the genes set forth in Fig. 2. In certain embodiments, the gene variant(s), for example, in a biological test sample, as referenced herein, is present in the sequence(s) of one or more of the genes set forth in Table 2 or Table 3.
  • the gene variant(s), for example in a biological test sample, as referenced herein, is present in one or more of AKTl, AKT2, AKT3, ARIDIA, NFl, PHLPP2, PIK3CA, PIK3R1, PTEN, RICTOR, RPTOR, STK11 (LKB1), TSC1, TSC2, PDK1, PRAS40, PRKDC, EIF4E, and EIF4EBP1.
  • the gene variant(s), for example in a biological test sample, as referenced herein, is not present in one or more of EGFR, IGF1R, IGF2R, KRAS, MYC, ERBB3, MET, PDGFRB, NOTCHl, MEK, BRAF, N-RAS, MAP3K8, BCL2, BCL2L11, BAD, MCL1, BIRC5, CCND1, ARAF, RAFl, CDC25A, MDM2, FOX03, GSK3B, and XIAP.
  • the patient has a variant in one or more genes from Table 2 or Table 3.
  • the gene variant(s), for example in a biological test sample, as referenced herein, is present in one or more of EGFR, ERBB2 (HER2), KIT, PDGFRA, PIK3CA, PTEN, DAXX, ATRX, MEN1, FGFR4, ARIDIA, KDMA6A, TP53, FGFR3, NF2, TSCl, CDKN2A, or MCL1.
  • the gene variant(s), for example in a biological test sample from a NET patient is present in one or more of EGFR, ERBB2 (HER2), KIT, PDGFRA, PIK3CA and PTEN.
  • the gene variant(s), for example in a biological test sample from a NET patient is present in one or more of DAXX, ATRX, MEN1, PIK3CA, PTEN, TP53, TSC2, and FGFR4.
  • the gene variant(s), for example in a biological test sample from a breast cancer patient is present in one or more of PIK3CA, PTEN, ARIDIA, and MCL1.
  • the gene variant(s), for example in a biological test sample from a metastatic bladder cancer patient is present in one or more of ARIDIA, KDMA6A, TP53, FGFR3, NF2, and TSCl .
  • the gene variant(s), for example in a biological test sample from a glioblastoma patient is present in one or more of PDGFRA, and CDKN2A.
  • the gene variant(s), for example in a biological test sample, as referenced herein, is present in one or more of ARIDIA, CEBPA, FGFR2, IGF1R, RICTOR, STKl 1, GPR124, TNFAIP3, CARDl 1, FANCA, KIT, JAK2 and BRAF.
  • the gene variant(s), for example in a biological test sample from a HCC patient is present in one or more of ARIDIA and CEBPA.
  • the gene variant(s), for example in a biological test sample from a solid tumor patient is present in one or more of ARIDIA, FGFR2, IGF1R, RICTOR, and STKl 1.
  • the gene variant(s), for example in a biological test sample from a HCC patient is present in GPR124.
  • the gene variant(s), for example in a biological test sample from a solid tumor patient is present in
  • the gene variant(s), for example in a biological test sample from a NSCLC patient, is present in one or more of TNFAIP3, APC, ARIDIA, CARDl 1, FANCA, and KIT.
  • the gene variant(s), for example in a biological test sample from a DLBCL patient is present in JAK2.
  • a patient or a patient's cancer is screened for gene mutation or variant(s) by obtaining a biological sample from said patient or said patient's cancer, and determining the gene sequence(s) of said sample ex vivo.
  • the ex vivo analysis is performed using microarray analysis or sequence based techniques, for example, Sanger sequencing, di-deoxy chain termination sequencing, massively parallel next generation sequencing (NGS), or PCR based methods.
  • technologies include Sanger sequencing (chain termination); pyrosequencing (sequencing by synthesis method); mass spectroscopy-based mutation analysis (MALDI-TOF); allele-specific RT PCR; and RT-PCR melting curve analysis.
  • NGS methods include flow-based, reversible dye termination and 4-color optical imaging; emulsion PCR with bead-based pyrosequencing and charge-coupled device (CCD) light imaging; oligo-dT captured PolyA-tailed DNA fragments, flow cell 4-color deoxynucleotide phosphate (dNTP) optical imaging; sequential dinucleotide ligation, flow cell-based 4-color optical imaging; and semiconductor-based nonoptical detection, standard dNTP sequencing chemistry (see J. Ross and M. Cronin, Am. J. Clin. Pathol, 136;527- 539 (2011)).
  • CCD charge-coupled device
  • the cancer characterized by a gene mutation or variant(s), for example, breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC is that in which the PI3K/mTOR pathway is activated.
  • the cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC is that in which the PI3K/mTOR pathway is activated due to PTEN loss, a PIK3CA mutation or EGFR overexpression, or a combination thereof.
  • the cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC is a cancer associated with the pathways involving mTOR, PI3K, or Akt kinases and mutants or isoforms thereof.
  • Other cancers within the scope of the methods provided herein include those associated with the pathways of the following kinases: ⁇ , ⁇ , ⁇ , KDR, GSK3a, GSK3 , ATM, ATX, ATR, cFMS, and/or DNA-PK kinases and mutants or isoforms thereof.
  • Solid Tumors for example, RECIST 1.1
  • a TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • the variant is in one or more of ARIDIA, CEBPA, FGFR2, IGFIR, RICTOR or STKl 1.
  • the patient is a HCC patient, and the variant is in ARIDIA, CEBPA or both.
  • the patient is a solid tumor patient, and the variant is in one or more of ARIDIA, FGFR2, IGFIR, RICTOR, and STKl 1.
  • the variant is in GPR124.
  • the patient is a solid tumor patient, for example, an HCC patient.
  • provided herein are methods to increase Progression Free Survival rates, as determined by Kaplan-Meier estimates.
  • the variant is in one or more of APC, ARIDIA, CARD11, FANCA, KIT, and JAK2.
  • the patient is an NSCLC patient and the variant is in one or more of APC,
  • the patient is a DLBCL patient and the variant is in JAK2.
  • a hematological cancer for example DLBCL (diffuse large B-cell lymphoma), ML (mantle cell lymphoma), FL (follicular lymphoma), and AML (acute myeloid leukemia), characterized by decreased IRF4 gene and/or protein expression, comprising screening a patient's cancer for the presence of decreased IRF4 gene and/or protein expression relative to wild type, and administering an effective amount of a TOR kinase inhibitor to the patient having a cancer characterized by low IRF4 gene and/or protein expression.
  • DLBCL diffuse large B-cell lymphoma
  • ML mantle cell lymphoma
  • FL follicular lymphoma
  • AML acute myeloid leukemia
  • TOR kinase inhibitor in a patient having a hematological cancer for example DLBCL (diffuse large B-cell lymphoma), ML (mantle cell lymphoma), FL (follicular lymphoma), and AML (acute myeloid leukemia), characterized by decreased IRF4 gene and/or protein expression
  • the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the IRF-4 gene and/or protein expression levels in said biological test sample; c) comparing said IRF4 gene and/or protein expression levels to the IRF4 gene and/or protein expression levels of a biological wild-type sample; wherein a decreased IRF4 gene and/or protein expression level indicates an increased likelihood of response to TOR kinase inhibitor treatment of said patient's cancer.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • a hematological cancer for example DLBCL (diffuse large B-cell lymphoma), ML (mantle cell lymphoma), FL (follicular lymphoma), and AML (acute myeloid leukemia), characterized by decreased IRF4 gene and/or protein expression
  • the method comprising: a) obtaining the IRF-4 gene and/or protein expression levels in said biological test sample; c) comparing said IRF-4 gene and/or protein expression levels to the IRF4 gene and/or protein expression levels of a biological wild-type sample; wherein a decreased IRF4 gene and/or protein level indicates an increased likelihood of therapeutic efficacy of said TOR kinase inhibitor treatment for said patient.
  • the method additionally comprises administering an effective amount of a TOR kinase inhibitor, as described herein.
  • a hematological cancer for example DLBCL
  • a hematological cancer for example DLBCL
  • TOR pathway activation for example, increased levels of one or more of p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, and pS6 S240/S244 and S235/S236, comprising screening a patient's cancer for the presence of increased levels of TOR pathway activation relative to wild type, for example, increased levels of one or more of p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, and pS6 S240/S244 and S235/S236 relative to wild type, and administering an effective amount of a TOR kinase inhibitor to the patient having a
  • TOR kinase inhibitor in a patient having a hematological cancer for example DLBCL, characterized by increased levels of TOR pathway activation, for example, increased levels of one or more of p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, and pS6 S240/S244 and S235/S236, the method comprising: a) obtaining a biological test sample from the patient's cancer; b) obtaining the TOR pathway activation levels, for example, the levels of one or more of p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, and pS6 S240/S244 and S235/S236, in said biological test sample; c) comparing said TOR pathway activation levels, for example
  • TOR pathway activation for example, increased levels of one or more of p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, and pS6 S240/S244 and S235/S236, the method comprising: a) obtaining the TOR pathway activation levels, for example, the levels of one or more of p-mTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, and pS6 S240/S244 and S235/S236, in said biological test sample; c) comparing said TOR pathway activation levels, for example, the levels of one or more of
  • Solid Tumors for example, RECIST 1.1
  • a TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • the prevention or delaying of progressive disease is characterized or achieved by a change in overall size of the target lesions, of for example, between -30% and +20% compared to pre-treatment.
  • the change in size of the target lesions is a reduction in overall size of more than 30%, for example, more than 50% reduction in target lesion size compared to pre-treatment.
  • the patient is a NSCLC patient and the variant is in TNFAIP3.
  • the prevention is characterized or achieved by a reduction in size or a delay in progression of non- target lesions compared to pre-treatment.
  • the prevention is achieved or characterized by a reduction in the number of target lesions compared to pre-treatment.
  • the prevention is achieved or characterized by a reduction in the number or quality of non-target lesions compared to pre-treatment.
  • the prevention is achieved or characterized by the absence or the disappearance of target lesions compared to pre-treatment.
  • the prevention is achieved or characterized by the absence or the disappearance of non- target lesions compared to pre-treatment.
  • the prevention is achieved or characterized by the prevention of new lesions compared to pre-treatment. In yet another embodiment, the prevention is achieved or characterized by the prevention of clinical signs or symptoms of disease progression compared to pre-treatment, such as cancer-related cachexia or increased pain.
  • TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • TOR kinase inhibitor administered to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • TOR kinase inhibitor administered to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, wherein the treatment results in a complete response, partial response or stable disease, as determined by Response Evaluation Criteria in Solid Tumors (for example, RECIST 1.1).
  • a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to a patient a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, wherein the treatment results in a reduction in target lesion size, a reduction in non-target lesion size and/or the absence of new target and/or non-target lesions, compared to pre-treatment.
  • a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, wherein the treatment results in prevention or retarding of clinical progression, such as cancer-related cachexia or increased pain.
  • COG Cooperative Oncology Group Performance Status of a patient, comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • a TOR kinase inhibitor for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • TOR kinase inhibitor in another embodiment, provided herein are methods for inducing a therapeutic response assessed by Positron Emission Tomography (PET) outcome of a patient, comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • PET Positron Emission Tomography
  • a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, wherein the treatment results in a reduction in tumor metabolic activity, for example, as measured by FDG-PET imaging.
  • the inhibition of phosphorylation is assessed in a biological sample of the patient, such as in circulating blood and/or tumor cells, skin biopsies and/or tumor biopsies or aspirate.
  • the amount of inhibition of phosphorylation is assessed by comparison of the amount of phospho- S6RP, 4E-BP1 and/or AKT before and after administration of the TOR kinase inhibitor.
  • kits for measuring inhibition of phosphorylation of S6RP, 4E-BP1 or AKT in a patient a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to said patient, measuring the amount of phosphorylated S6RP, 4E-BP1 and/or AKT in said patient, and comparing said amount of phosphorylated S6RP, 4E-BP1 and/or AKT to that of said patient prior to administration of an effective amount of a TOR kinase inhibitor.
  • the inhibition of phosphorylation of S6RP, 4E-BP1 and/or AKT is assessed in B-cells, T-cells and/or monocytes.
  • phosphorylation of S6RP, 4E-BP1 and/or AKT in a biological sample of a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to said patient and comparing the amount of phosphorylated S6RP, 4E-BP1 and/or AKT in a biological sample of a patient obtained prior to and after administration of said TOR kinase inhibitor, wherein less phosphorylated S6RP, 4E-BP1 and/or AKT in said biological sample obtained after administration of said TOR kinase inhibitor relative to the amount of
  • phosphorylated S6RP, 4E-BP1 and/or AKT in said biological sample obtained prior to administration of said TOR kinase inhibitor indicates inhibition.
  • the inhibition of phosphorylation of S6RP, 4E-BP1 and/or AKT is assessed in B-cells, T-cells and/or monocytes.
  • Inhibition of phosphorylation of S6RP (Ser235/236 and/or Ser240/244), 4E-BP1 (Thr37/46), and/or AKT (Ser473) can be measured by various methodology including flow cytometry, ELISA, immunohistochemistry (IHC), immunofluorescence (IF) using
  • DNA-PK DNA-dependent protein kinase
  • methods for inhibiting DNA-dependent protein kinase (DNA-PK) activity in a patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to said patient.
  • DNA-PK DNA-dependent protein kinase
  • DNA-PK inhibition is assessed in the skin of the patient having a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, in one example in a UV light-irradiated skin sample of said patient.
  • DNA-PK inhibition is assessed in a tumor biopsy or aspirate of a patient a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC.
  • inhibition is assessed by measuring the amount of phosphorylated DNA-PK S2056 (also known as pDNA-PK S2056) before and after administration of the TOR kinase inhibitor.
  • kits for measuring inhibition of phosphorylation of DNA-PK S2056 in a skin sample of a patient a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase inhibitor to said patient, measuring the amount of phosphorylated DNA-PK S2056 present in the skin sample and comparing said amount of phosphorylated DNA-PK S2056 to that in a skin sample from said patient prior to administration of an effective amount of a TOR kinase inhibitor.
  • the skin sample is irradiated with UV light.
  • DNA-PK DNA-dependent protein kinase
  • Inhibition of DNA-PK activity can be measured by monitoring phosphorylation of substrates of DNA-PK, such as DNA-PK itself and XRCC4. Inhibition of DNA-PK activity can also be measured by monitoring accumulation of double strand DNA damage in tissues and/or cells such as those mentioned above.
  • a cancer characterized by a gene mutation or variant(s), for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC comprising administering an effective amount of a TOR kinase to a patient having said cancer, wherein the treatment results in one or more of inhibition of disease progression, inhibition of tumor growth, reduction of primary tumor, relief of tumor- related symptoms, inhibition of tumor secreted factors (including tumor secreted hormones, such as those that contribute to carcinoid syndrome), delayed appearance of primary or secondary tumors, slowed development of primary or secondary tumors, decreased occurrence of primary or secondary tumors, slowed or decreased severity of secondary effects of disease, arrested tumor growth and regression of tumors, increased Time To Progression (TTP), increased Progression Free Survival (PFS), and/or increased Overall Survival (OS), among others.
  • TTP Time To Progression
  • PFS Progression Free Survival
  • OS Overall Survival
  • the TOR kinase inhibitor is a compound as described herein. In one embodiment, the TOR kinase inhibitor is a compound of formula (I). In one embodiment, the TOR kinase inhibitor is a compound from Table A. In one embodiment, the TOR kinase inhibitor is Compound 1 (a TOR kinase inhibitor set forth herein having molecular formula C21H27N5O3). In one embodiment, the TOR kinase inhibitor is Compound 2 (a TOR kinase inhibitor set forth herein having molecular formula CieHieNsO).
  • the TOR kinase inhibitor is Compound 3 (a TOR kinase inhibitor set forth herein having molecular formula C21H24N8O2). In one embodiment, the TOR kinase inhibitor is Compound 4 (a TOR kinase inhibitor set forth herein having molecular formula C20H25N5O3).
  • Compound 1 is 7-(6-(2-hydroxypropan-2-yl)pyridin-3-yl)-l-
  • Compound 2 is l-ethyl-7-(2-methyl-6-(lH-l ,2,4-triazol-3- yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3-b]pyrazin-2(lH)-one or a tautomer thereof, for example, l-ethyl-7-(2-methyl-6-(4H-l ,2,4-triazol-3-yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3-b]pyrazin- 2( 1 H)-one, or 1 -ethyl-7-(2-methyl-6-( 1 H- 1 ,2,4-triazol-5 -yl)pyridin-3 -yl)-3 ,4- dihydropyrazino[2,3-b]pyrazin-2(lH)-one.
  • Compound 3 is 7-(2-methyl- 6-(4H-l ,2,4-triazol-3-yl)pyridin-3-yl)-l-(2-(tetrahydro-2H-pyran-4-yl)ethyl)-3,4- dihydropyrazino[2,3-b]pyrazin-2(lH)-one.
  • Compound 4 is l-((tra/?5)-4- hydroxycyclohexyl)-7-(6-(2-hydroxypropan-2-yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3- b]pyrazin-2(lH)-one, alternatively named l-((lr,4r)-4-hydroxycyclohexyl)-7-(6-(2- hydroxypropan-2-yl)pyridin-3-yl)-3,4-dihydropyrazino[2,3-b]pyrazin-2(lH)-one.
  • Compound 4 is a metabolite of Compound 1.
  • a TOR kinase inhibitor is administered to a patient in combination with 5-azacitidine or erlotinib.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by known somatic variants in one or more of ARID2, CDKN2A/B, FAM123B, KDM5C, KEAP1, KRAS, LRP1B, ROS1, SMARCD1, STK11, or TP53.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by amplification variants in one or more of CDK6, EGFR, MCL1 or RICTOR.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by one or more variants of unknown significance in one or more of ALOX12B, ATR, BCL6, BRAF, CDHl, CDK6, EPHA5, ERBB4, FANCM, FAT3, FGF4, FGF6, FGFRl, FGFR2, FGFR3, FLTl, FLT4, GATA2, GPR124, GSK3B, IK3R2, IL7R, IRF4, IRS2, JAK1, KDR, KEAP1, LRP1B, MLL, MLL2, MYCN, NOTCH4, NSD1, NTRK1, NUP93, PDGFRA, PIK3CG, RAD51C, RARA, RET, SOCS1, TBX3, TET2, TIPARP, TRRAP, or
  • the TOR kinase inhibitor is administered to a patient in combination with 5-azacitidine, wherein the patient is an NSCLC patient, wherein the NSCLC is characterized by known somatic variants in one or more of KEAP1, KRAS, ROS1, or STK11.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by one or more variants of unknown significance in one or more of ALOX12B, CDHl, ERBB4, FAT3, FGF4, FGF6, IL7R, IRF4, JAK1, LRP1B, MLL, MLL2, NSD1, NTRK1, PDGFRA, SOCS1, TBX3, TET2, or TSC1.
  • the TOR kinase inhibitor is administered to a patient in combination with erlotinib, wherein the patient is an NSCLC patient, wherein the NSCLC is characterized by known somatic variants in one or more of ARID2, CDKN2A/B, FAM123B, KDM5C, LRP1B, SMARCD1, STK11, or TP53.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by amplification variants in one or more of CDK6, EGFR, MCL1 or RICTOR.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by one or more variants of unknown significance in one or more of ATR, BCL6, BRAF, CDK6, EPHA5, ERBB4, FANCM, FAT3, FGFRl, FGFR2, FGFR3, FLTl, FLT4, GATA2, GPR124, GSK3B, IK3R2, IRS2, KDR, KEAPl, LRPIB, MLL2, MYCN, NOTCH4, NUP93, PIK3CG, RAD51C, RARA, RET, TIPARP, or TRRAP.
  • the patient is an NSCLC patient, wherein the NSCLC is characterized by an EGFR mutation.
  • a TOR kinase inhibitor is administered to a patient in combination with an IMiD® immunomodulatory compound.
  • IMiD® immunomodulatory drugs include, but are not limited to, lenalidomide (REVLIMID®) pomalidomide (Actimid(TM);
  • the compound is:
  • the patient is a DLBCL patient.
  • a TOR kinase inhibitor can be combined with radiation therapy or surgery.
  • a TOR kinase inhibitor is administered to patient who is undergoing radiation therapy, has previously undergone radiation therapy or will be undergoing radiation therapy.
  • a TOR kinase inhibitor is administered to a patient who has undergone tumor removal surgery.
  • TOR kinase inhibitors and other active ingredients can be administered to a patient prior to, during, or after the occurrence of the adverse effect associated with conventional therapy.
  • NSCLC non-small cell lung cancer
  • GBM glioblastoma multiforme
  • HCC hepatocellular carcinoma
  • gastrointestinal neuroendocrine tumor of non-pancreatic origin NET
  • diffuse large B-cell lymphoma DLBCL
  • multiple myeloma MM
  • hormone receptor positive breast cancer HRPBC
  • administering an effective amount of a TOR kinase inhibitor to a patient having non-small cell lung cancer (NSCLC), glioblastoma multiforme (GBM), hepatocellular carcinoma (HCC), gastrointestinal neuroendocrine tumor of non-pancreatic origin (NET), diffuse large B-cell lymphoma (DLBCL), multiple myeloma (MM) or hormone receptor positive breast cancer (HRPBC), characterized by a particular gene mutation, relative to wild type.
  • NSCLC non-small cell lung cancer
  • GBM glioblastoma multiforme
  • HCC hepatocellular carcinoma
  • NET gastrointestinal neuroendocrine tumor of non-pancreatic origin
  • DLBCL diffuse large B-cell lymphoma
  • MM multiple myelom
  • the gene mutation occurs in one or more genes from Table 1, i.e. PIK3CA, RICTOR, TP53, IGF1R or PTEN.
  • the mutation is a mutation in one or more of RICTOR, TP53 or IGGF1R.
  • a further mutation is a mutation in PIK3CA.
  • the mutation is a mutation in the gene sequence of AKTl .
  • the mutation is a gene amplication mutation in the gene sequence of AKT2.
  • the mutation is a mutation in RICTOR.
  • the mutation is a mutation in TP53.
  • the mutation is a mutation in IGF1R. In some such
  • a further mutation results in PTEN loss.
  • the breast cancer is ER+.
  • the breast cancer is PR+.
  • the breast cancer is ER+/PR+.
  • methods for treating or preventing non-small cell lung cancer comprising administering an effective amount of a TOR kinase inhibitor to a patient having non-small cell lung cancer (NSCLC) characterized by a particular gene mutation, relative to wild type, wherein the mutation is a mutation in Rictor.
  • NSCLC non- small cell lung cancer
  • methods for treating or preventing non- small cell lung cancer comprising administering an effective amount of a TOR kinase inhibitor to a patient having non-small cell lung cancer (NSCLC) characterized by a particular gene mutation, relative to wild type, wherein the mutation is a mutation in RICTOR resulting in amplification of RICTOR.
  • NSCLC non-small cell lung cancer
  • GBM glioblastoma multiforme
  • HCC hepatocellular carcinoma
  • gastrointestinal neuroendocrine tumor of non-pancreatic origin NET
  • diffuse large B-cell lymphoma DLBCL
  • multiple myeloma MM
  • hormone receptor positive breast cancer HRPBC
  • administering an effective amount of a TOR kinase inhibitor to a patient having non-small cell lung cancer (NSCLC), glioblastoma multiforme (GBM), hepatocellular carcinoma (HCC), gastrointestinal neuroendocrine tumor of non-pancreatic origin (NET), diffuse large B-cell lymphoma (DLBCL), multiple myeloma (MM) or hormone receptor positive breast cancer (HRPBC), characterized by one or more variants, relative to wild type.
  • NSCLC non-small cell lung cancer
  • GBM glioblastoma multiforme
  • HCC hepatocellular carcinoma
  • NET gastrointestinal neuroendocrine tumor of non-pancreatic origin
  • DLBCL diffuse large B-cell lymphoma
  • MM multiple myelom
  • the variant occurs in one or more genes from Fig. 2, Table 2 or Table 3.
  • the variant is one or more known somatic-variants, likely-somatic variants, rearrangements, variants-of-unknown-significance, or copy-number variants, for example, amplifications or deletions, or a combination thereof.
  • the variant is one or more known somatic variants.
  • the variant is one or more likely somatic- variants.
  • the variant is one or more rearrangements.
  • the variant is one or more variants-of-unknown-significance.
  • the variant is one or more amplifications.
  • the variant is one or more deletions.
  • the variant is one or more known somatic variants of genes selected from AKT1, ATM, BRAF, CDKN2A, CTNNB1, ERBB2, ERBB4, ESR1, EZH2, FANCM, FBXW7, FGFRl, FGFR2, KRAS, MAP2K1, MLHl, MSH6, MTOR, PIK3CA, PTEN, TP53, TRRAP, and TSC2.
  • the variant is one or more known somatic variants of genes selected from AKT1, ATM, BRAF, CDKN2A, CTNNB1, ERBB2, ERBB4, ESR1, EZH2, FBXW7, FGFRl, FGFR2, KRAS, MAP2K1, MSH6, MTOR, PIK3CA, TP53, TRRAP, TSC2, or VHL.
  • the variant is one or more likely somatic-variants of genes selected from APC, ARIDIA, ASXL1, ATRX, BACH1, BRCA1, BRCA2, CDH1, DNMT3A, FAM123B, FLT3, IKZF1, NOTCH2, NOTCH3, PTEN, PTPRD, RBI, SMARCA4, STK11, TNFAIP3, TP53, or TSC1.
  • the variant is one or more likely somatic- variants of genes selected from APC, ARIDIA, ASXL1, ATRX, BRCA1, BRCA2, CDH1, DNMT3A, FAM123B, FLT3, IKZF1, NOTCH2, NOTCH3, PTEN, PTPRD, RBI, SMARCA4, STK11, TNFAIP3, TP53, or TSC1.
  • the variant is one or more rearrangements in genes selected from BRCA1, BRCA2, or FANCA.
  • the variant is one or more amplifications of genes selected from BCL2L1, CCNDl, CCNE1, EGFR, FGFRl, IGFIR, KDR, KIT, MCLl, MYC, MYST3, NKX2-1, PDGFRA, PIK3CA, RICTOR, SOX2, SRC, or ZNF217.
  • the variant is one or more amplifications of genes selected from BCL2L1, CCNDl, CCNE1, EGFR, FGFRl, IGFIR, KDR, KIT, MCLl, MYC, MYST3, NKX2-1, PDGFRA, PIK3CA, RICTOR, or SOX2.
  • the variant is one or more deletions in genes selected from
  • CDKN2A CDKN2A, or CDKN2B.
  • the variant is one or more deletions in genes selected from CDKN2A, CDKN2B, or TSC2.
  • the variant is one or more variants-of-unknown- significance in genes selected from ABLl, ABL2, AKTl, AKT3, ALK, APC, APCDDl , AR, ARAF, ARIDIA, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXL, BCL2, BCL6, BLM, BRAF, BRCA1, BRCA2, BRIPI, Cl lorOO, CARDl l, CBL, CCNDl, CCND3, CDC73, CDH2, CDH20, CDH5, CDK12, CDK4, CDK6, CDK8, CDKN2A, CDKN2C, CEBPA, CHEK1, CHEK2, CIC,
  • CREBBP CRKL
  • the variant is one or more variants-of-unknown-significance in genes selected from ABL1, ABL2, AKT1, AKT3, ALK, APC, APCDD1, AR, ARAF, ARID 1 A, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXL, BAP1, BCL2, BCL6, BLM, BRAF, BRCA1, BRCA2, BRIP1, Cl lorOO, CARD11, CBL, CCND1, CCND3, CDC73, CDH2, CDH20, CDH5, CDK12, CDK6, CDK8, CDKN2A, CDKN2C, CEBPA, CEBPA, CEBPA, CEBPA, CHEK1, CHEK2, CIC, CREBBP, CRKL, CTNNA1, CTNNB1, CUL4A, CUL4B, DAXX, DDR2, DNMT3A, DOT1L, EGFR, EPHA3, EPHA5, EPHA6, EPHA7, EPHB
  • compositions comprising an effective amount of a TOR kinase inhibitor and compositions comprising an effective amount of a TOR kinase inhibitor and a pharmaceutically acceptable carrier or vehicle.
  • the pharmaceutical composition described herein are suitable for oral, parenteral, mucosal, transdermal or topical administration.
  • the TOR kinase inhibitors can be administered to a patient orally or parenterally in the conventional form of preparations, such as capsules, microcapsules, tablets, granules, powder, troches, pills, suppositories, injections, suspensions and syrups.
  • Suitable formulations can be prepared by methods commonly employed using conventional, organic or inorganic additives, such as an excipient (e.g., sucrose, starch, mannitol, sorbitol, lactose, glucose, cellulose, talc, calcium phosphate or calcium carbonate), a binder (e.g., cellulose, methylcellulose,
  • hydroxymethylcellulose polypropylpyrrolidone, polyvinylpyrrolidone, gelatin, gum arabic, polyethyleneglycol, sucrose or starch
  • a disintegrator e.g., starch, carboxymethylcellulose, hydroxypropylstarch, low substituted hydroxypropylcellulose, sodium bicarbonate, calcium phosphate or calcium citrate
  • a lubricant e.g., magnesium stearate, light anhydrous silicic acid, talc or sodium lauryl sulfate
  • a flavoring agent e.g., citric acid, menthol, glycine or orange powder
  • a preservative e.g, sodium benzoate, sodium bisulfite, methylparaben or
  • propylparaben e.g., citric acid, sodium citrate or acetic acid
  • a suspending agent e.g., methylcellulose, polyvinyl pyrroliclone or aluminum stearate
  • a dispersing agent e.g., sodium citrate or acetic acid
  • the effective amount of the TOR kinase inhibitor in the pharmaceutical composition may be at a level that will exercise the desired effect; for example, about 0.005 mg/kg of a patient's body weight to about 10 mg/kg of a patient's body weight in unit dosage for both oral and parenteral administration.
  • the dose of a TOR kinase inhibitor to be administered to a patient is rather widely variable and can be patient to the judgment of a health-care practitioner.
  • the TOR kinase inhibitors can be administered one to four times a day in a dose of about 0.005 mg/kg of a patient's body weight to about 10 mg/kg of a patient's body weight in a patient, but the above dosage may be properly varied depending on the age, body weight and medical condition of the patient and the type of administration.
  • the dose is about 0.01 mg/kg of a patient's body weight to about 5 mg/kg of a patient's body weight, about 0.05 mg/kg of a patient's body weight to about 1 mg/kg of a patient's body weight, about 0.1 mg/kg of a patient's body weight to about 0.75 mg/kg of a patient's body weight or about 0.25 mg/kg of a patient's body weight to about 0.5 mg/kg of a patient's body weight.
  • one dose is given per day
  • two doses are given per day.
  • the amount of the TOR kinase inhibitor administered will depend on such factors as the solubility of the active component, the formulation used and the route of administration.
  • kits for the treatment or prevention of a disease or disorder comprising the administration of about 0.375 mg/day to about 750 mg/day, about 0.75 mg/day to about 375 mg/day, about 3.75 mg/day to about 75 mg/day, about 7.5 mg/day to about 55 mg/day or about 18 mg/day to about 37 mg/day of a TOR kinase inhibitor to a patient in need thereof.
  • the methods disclosed herein comprise the administration of 15 mg/day, 30 mg/day, 45 mg/day or 60 mg/day of a TOR kinase inhibitor to a patient in need thereof.
  • the methods disclosed herein comprise administration of 0.5 mg/day, 1 mg/day, 2 mg/day, 4 mg/day, 8 mg/day, 16 mg/day, 20 mg/day, 25 mg/day, 30 mg/day or 40 mg/day of a TOR kinase inhibitor to a patient in need thereof.
  • kits for the treatment or prevention of a disease or disorder comprising the administration of about 0.1 mg/day to about 1200 mg/day, about 1 mg/day to about 100 mg/day, about 10 mg/day to about 1200 mg/day, about 10 mg/day to about 100 mg/day, about 100 mg/day to about 1200 mg/day, about
  • the methods disclosed herein comprise the administration of 0.1 mg/day, 0.5 mg/day, 1 mg/day, 10 mg/day, 15 mg/day, 20 mg/day,
  • TOR kinase inhibitor 30 mg/day, 40 mg/day, 45 mg/day, 50 mg/day, 60 mg/day, 75 mg/day, 100 mg/day, 125 mg/day, 150 mg/day, 200 mg/day, 250 mg/day, 300 mg/day, 400 mg/day, 600 mg/day or 800 mg/day of a TOR kinase inhibitor to a patient in need thereof.
  • unit dosage formulations that comprise between about 0.1 mg and about 2000 mg, about 1 mg and 200 mg, about 35 mg and about 1400 mg, about 125 mg and about 1000 mg, about 250 mg and about 1000 mg, or about 500 mg and about 1000 mg of a TOR kinase inhibitor.
  • unit dosage formulation comprising about 0.1 mg, 0.25 mg, 0.5 mg, 1 mg, 5 mg, 10 mg, 15 mg, 20 mg, 30 mg, 45 mg, 50 mg, 60 mg, 75 mg, 100 mg, 125 mg, 150 mg, 200 mg, 250 mg, 300 mg, 400 mg, 600 mg or 800 mg of a TOR kinase inhibitor.
  • unit dosage formulations that comprise 0.1 mg, 0.25 mg, 0.5 mg, 1 mg, 2.5 mg, 5 mg, 10 mg, 15 mg, 20 mg, 30 mg, 35 mg, 50 mg, 70 mg, 100 mg, 125 mg, 140 mg, 175 mg, 200 mg, 250 mg, 280 mg, 350 mg, 500 mg, 560 mg, 700 mg, 750 mg, 1000 mg or 1400 mg of a TOR kinase inhibitor.
  • unit dosage formulations that comprise about 5 mg, about 15 mg, about 20 mg, about 30 mg, about 45 mg, and about 50 mg of a TOR kinase inhibitor.
  • a TOR kinase inhibitor can be administered once, twice, three, four or more times daily.
  • a TOR kinase inhibitor can be administered orally for reasons of convenience.
  • a TOR kinase inhibitor when administered orally, is administered with a meal and water.
  • the TOR kinase inhibitor is dispersed in water or juice (e.g., apple juice or orange juice) and administered orally as a suspension.
  • a TOR kinase inhibitor when administered orally, is administered in a fasted state.
  • the TOR kinase inhibitor can also be administered intradermally, intramuscularly, intraperitoneally, percutaneously, intravenously, subcutaneously, intranasally, epidurally, sublingually, intracerebrally, intravaginally, transdermally, rectally, mucosally, by inhalation, or topically to the ears, nose, eyes, or skin.
  • the mode of administration is left to the discretion of the health-care practitioner, and can depend in-part upon the site of the medical condition.
  • capsules containing a TOR kinase inhibitor without an additional carrier, excipient or vehicle.
  • compositions comprising an effective amount of a TOR kinase inhibitor and a pharmaceutically acceptable carrier or vehicle, wherein a pharmaceutically acceptable carrier or vehicle can comprise an excipient, diluent, or a mixture thereof.
  • a pharmaceutically acceptable carrier or vehicle can comprise an excipient, diluent, or a mixture thereof.
  • the composition is a pharmaceutical composition.
  • compositions can be in the form of tablets, chewable tablets, capsules, solutions, parenteral solutions, troches, suppositories and suspensions and the like.
  • Compositions can be formulated to contain a daily dose, or a convenient fraction of a daily dose, in a dosage unit, which may be a single tablet or capsule or convenient volume of a liquid.
  • the solutions are prepared from water-soluble salts, such as the hydrochloride salt.
  • water-soluble salts such as the hydrochloride salt.
  • all of the compositions are prepared according to known methods in pharmaceutical chemistry.
  • Capsules can be prepared by mixing a TOR kinase inhibitor with a suitable carrier or diluent and filling the proper amount of the mixture in capsules.
  • the usual carriers and diluents include, but are not limited to, inert powdered substances such as starch of many different kinds, powdered cellulose, especially crystalline and microcrystalline cellulose, sugars such as fructose, mannitol and sucrose, grain flours and similar edible powders.
  • Tablets can be prepared by direct compression, by wet granulation, or by dry granulation. Their formulations usually incorporate diluents, binders, lubricants and disintegrators as well as the compound. Typical diluents include, for example, various types of starch, lactose, mannitol, kaolin, calcium phosphate or sulfate, inorganic salts such as sodium chloride and powdered sugar. Powdered cellulose derivatives are also useful. In one embodiment, the pharmaceutical composition is lactose-free. Typical tablet binders are substances such as starch, gelatin and sugars such as lactose, fructose, glucose and the like.
  • Natural and synthetic gums are also convenient, including acacia, alginates, methylcellulose, polyvinylpyrrolidine and the like. Polyethylene glycol, ethylcellulose and waxes can also serve as binders.
  • a lubricant might be necessary in a tablet formulation to prevent the tablet and punches from sticking in the die.
  • the lubricant can be chosen from such slippery solids as talc, magnesium and calcium stearate, stearic acid and hydrogenated vegetable oils. Tablet
  • disintegrators are substances that swell when wetted to break up the tablet and release the compound. They include starches, clays, celluloses, algins and gums. More particularly, corn and potato starches, methylcellulose, agar, bentonite, wood cellulose, powdered natural sponge, cation-exchange resins, alginic acid, guar gum, citrus pulp and carboxymethyl cellulose, for example, can be used as well as sodium lauryl sulfate. Tablets can be coated with sugar as a flavor and sealant, or with film- forming protecting agents to modify the dissolution properties of the tablet. The compositions can also be formulated as chewable tablets, for example, by using substances such as mannitol in the formulation.
  • a TOR kinase inhibitor When it is desired to administer a TOR kinase inhibitor as a suppository, typical bases can be used. Cocoa butter is a traditional suppository base, which can be modified by addition of waxes to raise its melting point slightly. Water-miscible suppository bases comprising, particularly, polyethylene glycols of various molecular weights are in wide use.
  • the effect of the TOR kinase inhibitor can be delayed or prolonged by proper formulation.
  • a slowly soluble pellet of the TOR kinase inhibitor can be prepared and incorporated in a tablet or capsule, or as a slow-release implantable device.
  • the technique also includes making pellets of several different dissolution rates and filling capsules with a mixture of the pellets. Tablets or capsules can be coated with a film that resists dissolution for a predictable period of time. Even the parenteral preparations can be made long-acting, by dissolving or suspending the TOR kinase inhibitor in oily or emulsified vehicles that allow it to disperse slowly in the serum.
  • kits comprising a TOR kinase inhibitor.
  • kits comprising a unit dosage form comprising a TOR kinase inhibitor in a sealed container, wherein the unit dosage form comprises about 1 mg to about 100 mg of a TOR kinase inhibitor.
  • kits comprising a unit dosage form comprising a TOR kinase inhibitor in a sealed container, wherein the unit dosage form comprises about 5 mg, about 20 mg or about 50 mg of a TOR kinase inhibitor.
  • kits comprising a TOR kinase inhibitor and means for monitoring patient response to administration of said TOR kinase inhibitor.
  • the patient has a cancer, for example breast cancer characterized by a gene mutation, for example a mutation in one or more genes from Table 1.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Fig. 2.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Table 2 or Table 3.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes as described herein.
  • the patient response measured is inhibition of disease progression, inhibition of tumor growth, reduction of primary and/or secondary tumor(s), relief of tumor-related symptoms, improvement in quality of life, inhibition of tumor secreted factors (including tumor secreted hormones, such as those that contribute to carcinoid syndrome), delayed appearance of primary and/or secondary tumor(s), slowed development of primary and/or secondary tumor(s), decreased occurrence of primary and/or secondary tumor(s), slowed or decreased severity of secondary effects of disease, arrested tumor growth and/or regression of tumors.
  • tumor secreted factors including tumor secreted hormones, such as those that contribute to carcinoid syndrome
  • kits comprising a TOR kinase inhibitor and means for monitoring patient response to administration of said TOR kinase inhibitor, wherein said response is Response Evaluation Criteria in Solid Tumors (for example, RECIST 1.1) or Eastern Cooperative Oncology Group Performance Status (ECOG).
  • Solid Tumors for example, RECIST 1.1
  • ECOG Eastern Cooperative Oncology Group Performance Status
  • kits comprising a TOR kinase inhibitor and means for measuring the amount of inhibition of phosphorylation of S6RP, 4E-BP1 and/or AKT in a patient.
  • the kits comprise means for measuring inhibition of phosphorylation of S6RP, 4E-BP1 and/or AKT in circulating blood or tumor cells and/or skin biopsies or tumor biopsies/aspirates of a patient.
  • kits comprising a TOR kinase inhibitor and means for measuring the amount of inhibition of phosphorylation as assessed by comparison of the amount of phospho- S6RP, 4E-BP1 and/or AKT before, during and/or after administration of the TOR kinase inhibitor.
  • the patient has a cancer, for example breast cancer characterized by a gene mutation, for example a mutation in one or more genes from Table 1.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Fig. 2.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Table 2 or Table 3.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes as described herein.
  • kits comprising a TOR kinase inhibitor and means for measuring the amount of inhibition of DNA-dependent protein kinase (DNA-PK) activity in a patient.
  • the kits comprise means for measuring the amount of inhibition of DNA-dependent protein kinase (DNA-PK) activity in a skin sample and/or a tumor biopsy/aspirate of a patient.
  • the kits comprise a means for measuring the amount of pDNA-PK S2056 in a skin sample and/or a tumor biopsy/aspirate of a patient.
  • the skin sample is irradiated by UV light.
  • kits comprising a TOR kinase inhibitor and means for measuring the amount of inhibition of DNA-dependent protein kinase (DNA-PK) activity before, during and/or after administration of the TOR kinase inhibitor.
  • kits comprising a TOR kinase inhibitor and means for measuring the amount of phosphorylated DNA- PK S2056 before, during and/or after administration of the TOR kinase inhibitor.
  • the patient has a cancer, for example breast cancer characterized by a gene mutation, for example a mutation in one or more genes from Table 1.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Fig. 2.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Table 2 or Table 3.
  • the patient has a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes as described herein.
  • Inhibition of phosphorylation of S6RP, 4E-BP 1 , and/or AKT can be measured in blood, skin, tumor, and/or circulating tumor cells (CTCs) in blood by various methodology including flow cytometry, ELISA, immunohistochemistry (IHC) using phosphorylation-specific antibodies.
  • Inhibition of DNA-PK activity can be measured in blood, skin, and/or circulating tumor cells (CTCs) in blood by monitoring phosphorylation of substrates of DNA-PK, such as DNA-PK itself and XRCC4.
  • Inhibition of DNA-PK activity can also be measured by monitoring accumulation of double strand DNA damage in tissues and/or cells such as those mentioned above.
  • kits provided herein comprise an amount of a TOR kinase inhibitor effective for treating or preventing a cancer, for example breast cancer characterized by a gene mutation, for example a mutation in one or more genes from Table 1.
  • the kits provided herein comprise an amount of a TOR kinase inhibitor effective for treating or preventing a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Fig. 2.
  • kits provided herein comprise an amount of a TOR kinase inhibitor effective for treating or preventing a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes from Table 2 or Table 3.
  • the kits provided herein comprise an amount of a TOR kinase inhibitor effective for treating or preventing a cancer, for example breast cancer, DLBCL, GBM, HCC, MM, NET, or NSCLC, characterized by one or more gene variants, for example a variant in one or more genes as described herein.
  • kits provided herein comprise a TOR kinase inhibitor having the molecular formula CieHieNsO. In certain embodiments, the kits provided herein comprise Compound 1. [00242] In certain embodiments, the kits provided herein further comprise instructions for use, such as for administering a TOR kinase inhibitor and/or monitoring patient response to administration of a TOR kinase inhibitor.
  • mTOR HTR-FRET Assay The following is an example of an assay that can be used to determine the TOR kinase inhibitory activity of a test compound.
  • TOR kinase inhibitors were dissolved in DMSO and prepared as 10 mM stocks and diluted appropriately for the experiments. Reagents were prepared as follows:
  • Invitrogen mTOR (cat#PV4753) was diluted in this buffer to an assay concentration of 0.200 ⁇ g/mL.
  • ATP/Substrate solution 0.075 mM ATP, 12.5 mM MnCl 2 , 50 mM Hepes, pH 7.4,
  • Detection reagent solution 50 mM HEPES, pH 7.4, 0.01% Triton X-100, 0.01%
  • TOR kinase inhibitors were tested in the mTor HTR-FRET assay and were found to have activity therein, with certain compounds having an IC 50 below 10 ⁇ in the assay, with some compounds having an IC 50 between and 0.005 nM and 250 nM, others having an IC 50 between and 250 nM and 500 nM, others having an IC 50 between 500 nM and 1 ⁇ , and others having an IC 50 between 1 ⁇ and 10 ⁇ .
  • DNA-PK assay is performed using the procedures supplied in the
  • DNA-PK enzyme can be purchased from
  • Selected TOR kinase inhibitors as described herein have, or are expected to have, an IC 50 below 10 ⁇ in this assay, with some TOR kinase inhibitors as described herein having an IC 50 below 1 ⁇ , and others having an IC 50 below 0.10 ⁇ .
  • Compound 1 will be administered orally to subjects with solid tumors, non-
  • Compound 1 will be administered orally to determine safety and tolerability and to define the non-tolerated dose (NTD) and the maximum tolerated dose (MTD).
  • NTD non-tolerated dose
  • MTD maximum tolerated dose
  • Evaluations will include the extent of inhibition of phosphorylation of S6RP
  • the study population will consist of men and women, 18 years or older, with advanced NHL, MM, neuroendocrine tumors (the latter also accepting subjects aged 12 years or older) or advanced unresectable solid tumors, including subjects who have progressed on (or not been able to tolerate) standard therapy or for whom no standard anticancer therapy exists.
  • FFPE formalin- fixed, paraffin embedded
  • Type-specific criteria are in addition to, or supersede, above criteria where applicable: (a) Glioblastoma multiforme (GBM) or gliosarcoma, excluding WHO Grade IV oligoastrocytoma (has received prior treatment including radiation and/or chemotherapy, with radiation completed > 12 weeks prior to Day 1; planned salvage surgical tumor resection on Day 15 ⁇ 7 days, anticipated to yield > 200 mg tumor tissue; no prior or scheduled Gliadel ® wafer implant unless area of assessment and planned resection is outside the region previously implanted; no prior interstitial brachytherapy or stereotactic radiosurgery unless area of assessment and planned resection is outside the region previously treated; no enzyme-inducing anti-epileptic drugs (EIAED) such as carbamazepine, phenytoin, phenobarbital, or primidone within 14 days before Day 1; able to undergo repeated magnetic resonance imaging (MRI) scans; Availability of adequate FFPE archival tumor material (for
  • MM Multiple Myeloma
  • absolute neutrophil count > 1.0 x 10 9 /L; platelets (pit) > 60 x 10 9 /L in subjects in whom ⁇ 50% of bone marrow mononuclear cells are plasma cells or > 30 x 10 9 /L in subjects in whom > 50% of bone marrow mononuclear cells are plasma cells); (f) Diffuse large B-cell lymphoma (DLBCL) (histologically proven diffuse large B-cell non-Hodgkin's lymphoma; platelets (pit) > 60 x 10 9 /L for subjects in whom ⁇ 50% of bone marrow mononuclear cells are lymphoma cells, or > 30 x 10 9 /L for subjects in whom > 50% of bone marrow mononuclear cells are lymphoma cells; at least 4 weeks from last dose of therapeutic glucocorticosteroids; adrenal replacement doses of glucocorticosteroids (up to the equivalent of 10 mg daily prednisone) are allowed).
  • DLBCL Diff
  • exclusion criteria are: (1) Symptomatic central nervous system metastases (excluding GBM; subjects with brain metastases that have been previously treated and are stable for 6 weeks are allowed); (2) Known acute or chronic pancreatitis; (3) Subjects with any peripheral neuropathy > NCI CTCAE grade 2; (4) Subjects with persistent diarrhea or malabsorption > NCI CTCAE grade 2, despite medical management; (5) Impaired cardiac function or clinically significant cardiac diseases, including any of the following: LVEF ⁇ 45% as determined by MUGA scan or ECHO, Complete left bundle branch, or bifasicular, block, Congenital long QT syndrome, Persistent or clinically meaningful ventricular arrhythmias or atrial fibrillation, QTcF > 460 msec on screening ECG (mean of triplicate recordings), Unstable angina pectoris or myocardial infarction ⁇ 3 months prior to starting Compound 1 , Other clinically significant heart disease such as
  • Child-bearing potential defined as sexually mature women who have not undergone a hysterectomy or bilateral oophorectomy, or who have not been naturally postmenopausal (ie., who have not menstruated at all) for at least 24 consecutive months; (b) males (with partners who are female with child-bearing potential must agree that they or their partners will use at least two effective contraceptive methods (including one barrier method) when engaging in reproductive sexual activity throughout the study, and will avoid conceiving for 28 days after taking the last dose of Compound 1 ; (1 1) Subjects with known HIV infection; (12) Known chronic hepatitis B or C virus (HBV/HCV) infection, unless comorbidity in subjects with HCC; (13) Any significant medical condition, laboratory abnormality, or psychiatric illness that would prevent the subject from participating in the study; (14) Any condition including the presence of laboratory abnormalities, which places the subject at unacceptable risk if he/she were to participate in the study; (15) Any condition that confound
  • exclusion criteria are:
  • Compound 1 will be supplied in appropriate strengths (e.g., 2.5 mg, 10 mg, and 20 mg) containing only the active pharmaceutical ingredient in reddish-brown gelatin capsules for oral administration. No other excipients will be used in the product capsules.
  • Compound 1 will be administered orally, in an uninterrupted once-daily schedule with no rest period between cycles. A dose of 7.5 mg/day of Compound 1 will be the starting dose in this protocol. Each dose will be taken in the morning. On clinic visit days, Compound 1 will be administered in the clinic after any predose tests have been completed. Food will be taken after all fasting tests have been completed (3 hours after dosing on Day 8). In cases where troublesome GI symptoms, fatigue or other symptoms persist beyond the end of Cycle 1 , dosing may be moved to the end of day. Compound 1 may be taken up to 12 hours late if dosing has been delayed on a single day; otherwise that day's dose should be omitted.
  • NTD non-tolerated dose
  • a dose will be considered to be non-tolerated if 2 evaluable subjects in a dose cohort experience dose-limiting toxicity (DLT).
  • DLT dose-limiting toxicity
  • NTD dose-limiting toxicity
  • MTD dose-limiting toxicity
  • An intermediate dose i.e., one between the NTD and the last dose level before the NTD
  • additional subjects within any dose cohort may be required to determine the MTD more precisely.
  • subjects may start Compound 1 at the MTD and/or a lower dose level based on safety, PK and PD data from Part A. Approximately 150 subjects will be treated and evaluated for safety and preliminary antitumor activity after every two cycles of therapy.
  • Tumor types include non-small cell lung cancer (NSCLC), glioblastoma multiforme (GBM),
  • HCC hepatocellular carcinoma
  • NET gastrointestinal neuroendocrine tumor of non-pancreatic origin
  • DLBCL diffuse large B-cell lymphoma
  • MM multiple myeloma
  • HRBC hormone receptor positive breast cancer
  • Cycle 1 30 days.
  • subjects are treated in 28-day cycles with continuous dosing from Day 1 to 28.
  • subjects will receive continuous dosing for 28 days from the beginning— there is neither an initial observation period nor a 48-hour PK collection.
  • Therapy may be discontinued if there is evidence of disease progression, but subjects can continue to receive Compound 1 as long as the Investigator considers they are deriving benefit from treatment. Therapy will be discontinued if there is unacceptable toxicity or if the subject decides to withdraw from the study.
  • the next lower dose level will be selected. Two dose reductions are allowed. For the starting dose level (7.5 mg) in Part A, reductions will be in 2.5 mg decrements. In Part B, for subjects starting at 45 mg QD dose reductions to 30 mg and 15 mg QD are permitted; for those starting at 30 mg QD, the dose reductions are 15 mg QD and 7.5 mg QD. If any subject continues to experience unacceptable toxicity after 2 dose reductions in Part A, Compound 1 will be discontinued permanently. In Part B, subjects may dose reduce up to 2 levels and increase again if clinically appropriate; subsequent dose reductions are permitted in the event of recurrent toxicity but, in such circumstances, it is not permitted to reescalate the dose again. For subjects in Part B starting at 30 mg QD, dose escalation to 45 mg QD is not allowed.
  • Tumor assessments including imaging (CT, MRI and/or PET) of the chest and abdomen and other sites as appropriate, will be performed during Screening. Subjects with brain lesions will also have brain scans at Screening and during follow-up tumor assessments. After Screening, tumor assessments (for all tumors except multiple myeloma) will be performed on completion of Cycles 2, 4 and 6 (i.e., on Cycles 3, 5 and 7/Day 1 ⁇ 7 days) and then every 3 months thereafter (e.g., Cycle 10 and 13/Day 1 ⁇ 7 days).
  • Tumor assessment for multiple myeloma and only NHL/DLBCL with known or suspected marrow involvement
  • NHL/DLBCL with known or suspected marrow involvement
  • PD biomarker analysis cytogenetic analysis if abnormally present at Screening
  • Tumor response will be based on Response Evaluation Criteria in Solid Tumors (RECIST 1.1), International Workshop Criteria (IWG) for NHL/DLBCL or International Uniform Response Criteria (IURC) for Multiple Myeloma, and RANO for GBM, using the post resection MRI scan as the baseline.
  • the primary efficacy endpoint for GBM will be the proportion of subjects progression-free at 6 months from Day 1 relative to efficacy evaluable subjects in the GBM type.
  • Subjects will be evaluated for tumor response on completion of Cycle 2, 4, 6, and so on.
  • a descriptive analysis of evidence of anti-tumor activity will be provided based on clinical and radiographic assessments by the investigator, which includes assessment of target lesion, non-target lesion, new lesion and overall response.
  • efficacy variables to be analyzed include tumor response at the end of treatment, the proportion of subject alive and progression-free, and duration of response. Efficacy variables will mature when last subject of a treatment arm or cohort have withdrawn from the study or completed 6 cycles.
  • Progression Free Survival rates will be computed using the Kaplan-Meier estimates. Duration of response will also be reported in subjects who respond, using tumor specific evaluation criteria. Two-sided 90% CIs of the Response Rate (RR), Disease Control Rate (DCR) and of the Progression Free Survival (PFS) rate at time of each scheduled response assessment (ie., Cycles 2, 4, 6, etc.) will be provided by tumor type..
  • RR Response Rate
  • DCR Disease Control Rate
  • PFS Progression Free Survival
  • mTOR biomarker inhibition in blood and tumor includes histopathologic response, correlations with pharmacogenomic findings and percentage of inhibition of pAKT (Ser473), phospho-S6RP (Ser235/236 and/or Ser240/244), phospho-4EB-Pl (Thr37/46), and/or other relevant biomarkers in peripheral blood samples and tumor, adverse events and clinical outcome.
  • the pharmacodynamic (PD) measurements are incorporated in this study to evaluate target inhibition of mTORCl and mTORC2 pathways, the consequences of such inhibition, and PK/PD relationships.
  • biomarker analysis will involve measuring pAKT (mTORC2) in protein lysates derived from isolated platelets.
  • the safety variables for this study are adverse events, clinical laboratory variables,
  • Part A the decision to either evaluate a higher dose level or declare a MTD will be determined by the Safety Review Committee (SRC) each time all clinical and laboratory safety data for a given cohort is available for review. The SRC will also determine the dose, doses, or schedule appropriate for Part B. During Part B, the SRC will continue to review safety data regularly and make recommendations about the study continuation, as appropriate.
  • SRC Safety Review Committee
  • patients undergoing the clinical protocol provide herein will show a positive tumor response, such as inhibition of tumor growth or a reduction in tumor size. In certain embodiments, patients undergoing the clinical protocol provide herein will show an improvement in brain lesions, such as a decrease in number or size. In certain embodiments, patients undergoing the clinical protocol provide herein will achieve a Response Evaluation Criteria in Solid Tumors (for example, RECIST 1.1) of complete response, partial response or stable disease. In certain embodiments, patients undergoing the clinical protocol provided herein will prevent a Response Evaluation Criteria in Solid Tumors (RECIST 1.1) of progressive disease. In certain embodiments, patients undergoing the clinical protocol provide herein will show an improvement in International Workshop Criteria (IWC) or International Uniform
  • patients undergoing the clinical protocol provide herein will show an improvement in Response Assessment for Neuro-Oncology (RANO) Working Group criteria.
  • patients undergoing the clinical protocol provide herein will show an improvement in ECOG performance status or PET outcomes.
  • patients undergoing the clinical protocol provide herein will show a reduction in a carcinoid syndrome-related symptom, for example, one or more of flushing, diarrhea, joint pain, bone pain, colicky abdominal pain, fatigue, wheezing, rash, cough, shortness of breath, edema or hypertension.
  • TOR Pathway biomarker measurements in whole blood Blood samples received from clinical sites were aliquoted into a 96-deepwell plate and rested for 1 hour at 37 °C. The samples were stimulated with anti-IgD and LPS for 15 minutes at 37 °C. The red blood cells were lysed and the white blood cells were fixed with BD Lyse/Fix Buffer at a ratio of 15: 1 buffer to blood for 10 minutes at 37 °C. The plates were centrifuged, aspirated, and 1 mL of ice-cold methanol was added to the wells containing fixed white blood cells to permeabilize the cells for intracellular staining. The plates were stored overnight at -80 °C.
  • the plates were thawed, centrifuged, aspirated and washed twice with PBS + 0.5% BSA.
  • the cells were stained with antibodies specific for the surface markers CD3, CD 14, and CD 19, and for mTOR pathway markers, including pS6 (S235/236), ⁇ 4 ⁇ 1 (T37/46), and pAKT (S473).
  • the cells were washed twice with PBS and fixed with 1.6% PFA.
  • Sample analysis The samples were analyzed on an 8 color cytometer. Control wells of 8-peak rainbow beads (Spherotech Libertyville, IL) were acquired at multiple points during sample acquisition. The median fluorescence intensity (MFI) was computed for each marker from the fluorescence intensity levels in T cells, B cells, and monocytes. The MFI were normalized using the 8-peak rainbow beads and presented as ERF (Equivalent number of
  • ERFs were calculated from the MFIs using a linear regression transformation carried out on a log-log scale using the rainbow calibration particles with 8 intensities on 8 colors.
  • the percent change from baseline for pS6, p4EBPl, and pAKT in stimulated and non-stimulated T cells, B cells, and monocytes was determined for each patient.
  • the baseline value was an average of two visits (screening and cycle 1/day -1 at 0 hr pre-dose) when available.
  • DNA Extraction Selected frozen or fixed tissue and tumor content was enriched to an estimated 50% in the selected frozenblock, sections of 20 ⁇ were cut in a cryostat and were disrupted and homogenized chemically (added in RLT plus buffer (Qiagen, Courtaboeuf, France) with ⁇ -mercaptoethanol (Sigma Aldrich, Saint-Quentin Fallavier, France). The disruption was finalized mechanically, in ice, with a Rotor-stator homogenizer (Kimble Chase Scientific, Vineland, New Jersey). The extraction was performed with the AllPrep DNA/RNA Mini Kit (Qiagen) for simultaneous purification of genomic DNA and total RNA from the same tissue sample.
  • NGS DNA Library Construction and Hybrid Capture Molecular barcode- indexed, ligation-based sequencing libraries were constructed by using 200 ng of sheared DNA or total DNA recovered from the sample (if >50 ng) when 200 ng was not available. Libraries were hybridization captured with custom biotinylated RNA oligo pools (custom SureSelect kit, Agilent) representing 3,230 exons in 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer (189 genes total, seven genes were screened across both exons and introns).
  • Genome Analysis Toolkit A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res 20: 1297-1303, 2010). Genomic base substitutions and indels were detected by using custom tools optimized for mutation calling in heterogeneous tumor samples on the basis of statistical modeling of sequence quality scores and local sequence assembly.
  • Variations were filtered by using dbSNP_135 (http:// www.ncbi.nlm.nih.gov/projects/SNP/) and a custom artifact database (Foundation Medicine, artifact databases 2011 through 2013) and were then annotated for known and likely somatic mutations by using COSMIC (see Forbes SA, Bindal N, Bamford S, et al: COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39:D945-D950, 2011). Copy number alterations were detected by comparing targeted genomic DNA sequence coverage with a process-matched normal control sample.
  • Genomic rearrangements were detected by clustering chimeric reads mapping to targeted introns. To maximize mutation-detection sensitivity, the test was validated to detect base substitutions at a > 10% mutant allele frequency with > 99% sensitivity and to detect indels at a > 20% mutant allele frequency with >95% sensitivity, with a false discovery rate of less than 1%. Recurrent somatic alterations were defined as genomic alterations in genes that are mutated > 5% in
  • DNA was extracted using DNeasy (Qiagen); concentration was determined by using Qubit® 2.0 Fluorometer (Invitrogen).
  • the exons 10 and 21 ofPIK3CA gene (NM 006218.2) and exon 4 ⁇ gene (NM 005163.2) were sequenced using direct Sanger sequencing approach after PCR amplification as previously validated by each platform to cover efficiently mutational hotspot mutation (p.Glu542Lys, p.Glu545Lys p.Hisl047Arg, p.Hisl0471eu for PI3KCA and p.Glul7Lys for AKT1) . Briefly, sequencing was performed after Polymerase Chain Reaction (PCR) amplification of targeted exons and use of the BigDye® Terminator Cycle Sequencing Kit (ref PMID: 22840369).
  • PCR Polymerase Chain Reaction
  • Sequencing reactions were analyzed on 48-capillary 3730 DNA Analyzer®. Sequences reading and alignment were performed with SeqScape® software (Applied Biosystems, Forster City, CA). Gene copy number alterations were quantified on Agilent 4* 180K or Affymetrix SNP 6.0. For each sample, 500 ng of DNA were fragmented by a double enzymatic digestion (Alul + Rsal) and controlled using 2100 Bioanalyzer System (Agilent Technologies). For genomic analyses on Agilent platforms, tumour DNA and control DNA (Human Genomic DNA Female G152Aand Male G147A) were labelled by random priming with CY5-dCTP and CY3-dCTP respectively.
  • Genomic analysis conducted on Affymetrix SNP6.0 arrays were achieved according Affymetrix protocol using 500ng of DNA as imput. When low amount of genomic DNA was available, 10-30ng of genomic DNA was used to perform a pre-amplification step using a phi29 modified protocol (Qiagen, REPLI-g Mini Kit, part number 150023, Courtaboeuf, France). To assume robustness of data, a normal genomic DNA was used in any batch of genomic analysis to validate the use of genomic profile of tumor samples. Genomic data are publicly available at Sage Bionetwork (Synapse ID: syn2286494).
  • PIK3CA/AKT1 mutation or an amplification ((Log 2 (ratio)>0.584 on Affymetrix-SNP6, and Log 2 (ratio)>0.887 on Agilent-4xl80K) ) of a gene encoding for a protein located in a pathway targeted by a drug.
  • the cut-off was chosen based on a previous pilot study (Arnedos et al, 2012, "Array CGH and PIK3CA/AKT1 mutations to drive patients to specific targeted agents: a clinical experience in 108 patients with metastatic breast cancer," Eur J Cancer 48: 2293-9).
  • the CGH array profile was discussed during a webconference to identify targetable genomic alterations.
  • a gene gain or deletion could be identified as targetable if the CGH array peak was indicative of alteration.
  • Log 2 Ratios were computed against hapmap270 using the Affymetrix Genotyping ConsoleTM software.
  • Agilent data Log 2 Ratios were computed as Log 2 (sample/reference) intensities, after adjusting cyanine signal biases.
  • EM expectation-maximisation algorithm
  • Compound 1 Administered Orally to Subjects with Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Multiple Myeloma.
  • Compound 1 is administered orally to subjects with advanced solid tumors, non-
  • the primary objectives of the study are (a) to determine the safety and tolerability of Compound 1 when administered orally and to define the non-tolerated dose (NTD) and the maximum tolerated dose (MTD) and (b) to determine the preliminary pharmacokinetics (PK) of Compound 1 following both single and multiple oral dosing of Compound 1.
  • the secondary objectives of the study are: (a) to evaluate the extent of inhibition of phosphorylation of S6RP (Ser235/236 and/or Ser240/244) and/or 4EB-P1 (Thr37/46) for mTORCl activity and AKT (Ser473) and/or other relevant biomarkers for mTORC2 activity in peripheral blood samples and tumor biopsies following treatment with Compound 1 ; (b) to provide information on the preliminary efficacy of Compound 1 ; and (c) to characterize PK of the metabolite of Compound 1 following oral dosing of Compound 1.
  • Compound 1 is administered orally to subjects with advanced solid tumors, non-
  • NTD non-tolerated dose
  • MTD non-tolerated dose
  • An intermediate dose ie, one between the NTD and the last dose level before the NTD
  • additional subjects within any dose cohort may be required to more precisely determine the MTD.
  • subjects may start Compound 1 at the MTD and/or a lower dose level based on safety, PK and PD data from Part A. Approximately 200 subjects will be treated and evaluated for safety and preliminary antitumor activity after every two cycles of therapy.
  • Selected tumor types include non-small cell lung cancer (NSCLC), glioblastoma multiforme (GBM), hepatocellular carcinoma (HCC), gastrointestinal neuroendocrine tumor (NET) of nonpancreatic origin, hormone receptor positive breast cancer (HRPBC), diffuse large B-cell lymphoma (DLBCL), and multiple myeloma (MM).
  • NSCLC non-small cell lung cancer
  • GBM glioblastoma multiforme
  • HCC hepatocellular carcinoma
  • NET gastrointestinal neuroendocrine tumor
  • HRPBC hormone receptor positive breast cancer
  • DLBCL diffuse large B-cell lymphoma
  • MM multiple myeloma
  • Part A cycles subjects are treated in 28-day cycles with continuous dosing from Day 1 to 28.
  • Part B subjects receive continuous dosing for 28 days from the beginning— there is neither an initial observation period nor a 48-hour PK collection.
  • Therapy may be discontinued if there is evidence of disease progression, but subjects can continue to receive Compound 1 as long as the Investigator considers they are deriving benefit from treatment. Therapy will be discontinued if there is unacceptable toxicity or if the subject decides to withdraw from the study.
  • Enrollment is expected to occur over approximately 36 months. Completion of active treatment and subject follow-up is expected to take up to an additional 24 months.
  • Part A the dose escalation phase
  • the dose level will start at 7.5 mg once daily. After the first dose is administered in any cohort, subjects are observed for at least 30 days before the next higher, protocol-specified dose cohort can begin. Intra-subject dose escalation is not permitted unless approved by the Safety Review Committee (SRC). The total number of subjects in Part A depends on the number of dose cohorts needed to establish the MTD.
  • SRC Safety Review Committee
  • subjects may receive Compound 1 at the MTD and/or a lower dose level, based on safety, PK and PD evaluations from Part A. Approximately 200 subjects (preselected tumor types in groups of up to 40) evaluable subjects will be evaluated for safety and preliminary antitumor effects.
  • Tumor response will be based on investigator assessment using Response Evaluation Criteria in Solid Tumors (RECIST 1.1), International Workshop Criteria (IWC) for NHL/DLBCL, International Uniform Response Criteria for Multiple Myeloma (IURC), or Responses Assessment for Neuro-Oncology (RANO) Working Group for GBM.
  • Secondary endpoints include mTOR biomarker inhibition in blood and tumor, histopathologic response and correlations with pharmacogenomic findings. Supplementary efficacy variables (eg, ECOG performance status, PET outcomes) will also be examined.
  • Safety assessments are adverse events, clinical laboratory variables, 12-lead ECGs (centrally reviewed), LVEF assessments, physical examinations, vital signs, concomitant medications/procedure assessments, and pregnancy status.
  • Part A the decision to either evaluate a higher dose level or declare a MTD will be determined by the SRC each time all clinical and laboratory safety data for a given cohort is available for review. The SRC will also determine the dose, doses, or schedule appropriate for Part B. During Part B, the SRC will continue to review safety data regularly and make recommendations about the study continuation, as appropriate.
  • Inclusion Criteria For both the dose escalation and dose expansion parts of this protocol: (a) understand and voluntarily sign an informed consent document prior to any study related assessments/procedures are conducted; (b) men and women, 18 years or older, with histologically or cytologically-confirmed, advanced NHL, MM, or advanced unresectable solid tumors including subjects who have progressed on (or not been able to tolerate) standard anticancer therapy or for whom no standard anticancer therapy exists; (c) ECOG PS of 0 or 1 for subjects with solid tumors, and 0 - 2 for hematologic malignancies; (d) subjects must have the following laboratory values: Absolute Neutrophil Count (ANC) > 1.5 x 10 9 /L; hemoglobin (Hgb) > 9 g/dl; platelets (pit) > 100 x 10 9 /L; potassium within normal limits or correctable with supplements; AST/SGOT and ALT/SGPT ⁇ 2.5 x Upper Limit of Normal (ANC) > 1.5
  • Part B For the dose expansion part (Part B) of this protocol: (a) retrieval of FFPE archival tumor tissue, either in tumor blocks or sectioned/mounted specimens for gene mutation and/or IHC biomarker assay for all tumors except MM. Only in exceptional circumstances may an exemption waiver be granted by the Sponsor for other tumor types; (b) satisfactory screening biopsy for gene mutation and/or IHC biomarker assay for accessible tumors for all tumors except NSCLC and NET (optional), and GBM; (c) Histologically-confirmed tumors of the following types, all with measurable disease.
  • Type-specific criteria are in addition to, or supersede, above criteria where applicable: (i) Non-small cell lung cancer (NSCLC); (ii) Glioblastoma multiforme (GBM) or gliosarcoma, excluding WHO Grade IV oligoastrocytoma: has received prior treatment including radiation and/or chemotherapy, with radiation completed > 12 weeks prior to Day 1; planned salvage surgical tumor resection on Day 15 ⁇ 7 days, anticipated to yield > 200 mg tumor tissue; no prior or scheduled Gliadel ® wafer implant unless area of assessment and planned resection is outside the region previously implanted; no prior interstitial brachytherapy or stereotactic radiosurgery unless area of assessment and planned resection is outside the region previously treated; no enzyme -inducing anti-epileptic drugs (EIAED) such as carbamazepine, phenytoin, phenobarbital, or primidone within 14 days before Day 1; able to undergo repeated magnetic resonance imaging (MRI) scans
  • HRPBC Hormone receptor-positive breast cancer
  • Exclusion Criteria For both the dose escalation and dose expansion parts of this protocol: (a) symptomatic central nervous system metastases (excluding GBM, per Inclusion Criterion 6c). Subjects with brain metastases that have been previously treated and are stable for 6 weeks are allowed; (b) known acute or chronic pancreatitis; (c) subjects with any peripheral neuropathy > NCI CTCAE grade 2; (d) subjects with persistent diarrhea or malabsorption > NCI CTCAE grade 2, despite medical management; (e) impaired cardiac function or clinically significant cardiac diseases, including any of the following: LVEF ⁇ 45 %> as determined by MUGA scan or ECHO; complete left bundle branch, or bifasicular, block; congenital long QT syndrome; persistent or clinically meaningful ventricular arrhythmias or atrial fibrillation; QTcF > 460 msec on screening ECG (mean of triplicate recordings); unstable angina pectoris or myocardial infarction ⁇ 3 months prior to starting Compound
  • Subjects must have recovered from any effects of recent radiotherapy that might confound the safety evaluation of study drug; (i) subjects who have undergone major surgery ⁇ 2 weeks prior to starting study drug or who have not recovered from side effects of such therapy; (j) women who are pregnant or breast feeding.
  • Females of child-bearing potential defined as sexually mature women who have not undergone a
  • hysterectomy or bilateral oophorectomy or who have not been naturally postmenopausal (ie, who have not menstruated at all) for at least 24 consecutive months; males with partners who are female with child-bearing potential must agree that they or their partners will use at least two effective contraceptive methods (including one barrier method) when engaging in reproductive sexual activity throughout the study, and will avoid conceiving for 28 days after the last dose of Compound 1;
  • Part B concurrent active second
  • Inhibitor Compound 1 in combination with erlotinib or oral azacitidine in advanced non-small cell lung cancer.
  • Compound 1 when administered orally in combination with either erlotinib or oral azacitidine and to define the non-tolerated dose (NTD) and the maximum tolerated dose (MTD) of each combination using NCI CTCAE v4; and to characterize the pharmacokinetics (PK) of Compound 1 and azacitidine following oral administration as single agents and after combination treatment.
  • the secondary objectives of the study are to evaluate the effect of study drugs on mTORCl and mTORC2 pathway biomarkers in blood and tumor; provide information on the preliminary efficacy of each drug combination; and characterize the PK of Compound 1 Ml metabolite after oral administration of Compound 1 as a single agent and in combination with erlotinib or oral azacitidine.
  • Compound 1 (15 mg, 30 mg, and 45 mg) concurrently with one or more dose levels of oral azacitidine (200 mg or 300 mg, as two or three 100 mg tablets) administered on Day 1 to 21 of each 28-day cycle after an initial single dose of Compound 1 seven days before, and a single dose of oral azacitidine on the first day of, the first cycle.
  • oral azacitidine 200 mg or 300 mg, as two or three 100 mg tablets
  • a standard "3 + 3" dose escalation design will be used to identify initial toxicity of each combination. Subjects will be assigned to study treatment arms based on Investigator choice and open slots. Cohorts of 3 subjects will take study drugs in defined dose increments and, in the event of dose-limiting toxicity (DLT) in 1 of 3 evaluable subjects, cohorts will be expanded to 6 subjects.
  • DLT dose-limiting toxicity
  • An evaluable subject for DLT is defined as one that received at least 20 of the 27 planned doses of Compound 1, and 21 of the 28 planned doses of erlotinib, during Cycle 1 in Arm A; received at least 20 of the 27 planned doses of Compound 1, and 14 of 21 planned doses of oral azacitidine, during Cycle 1 in Arm B; received at least 14 of 21 planned doses of Compound 1, and 6 of 7 planned doses of oral azacitidine, during Cycle 1 in Arm C; experienced study drug- related DLT after receiving at least one dose.
  • Non-evaluable subjects not due to DLT will be replaced. Additional subjects within any dose cohort may be enrolled at the discretion of the Safety Review Committee (SRC).
  • SRC Safety Review Committee
  • a dose will be considered the NTD when 2 of 6 evaluable subjects in a cohort experience drug-related DLT in Cycle 1.
  • the MTD is defined as the last dose level below the NTD with 0 or 1 out of 6 evaluable subjects experiencing DLT during Cycle 1. If 2 of 6 DLT are observed at the first dose level with either combination, a lower dose combination may be explored at the discretion of the SRC.
  • An intermediate dose of Compound 1 (one between the NTD and the last dose level before the NTD) may be evaluated to accurately determine the MTD of the combination.
  • each combination treatment arm will be expanded with approximately 10 additional evaluable subjects. Expansion may occur at the MTD established in the dose escalation phase, or at an alternative tolerable combination dose level, based on the review of safety, PK and PD data.
  • Tumor biopsy for analysis of genetic mutations and biomarkers of treatment activity is optional in the dose escalation phase but mandatory during the dose expansion phase. Paired tumor biopsies to evaluate tumor biomarkers of Compound 1 , erlotinib and/or oral azacitidine activity will be required in the expansion cohorts.
  • the study population will consist of men and women, 18 years or older, with Stage
  • IIIB/IV NSCLC with disease progression following at least one standard first-line treatment regimen.
  • First-line treatment may include either chemotherapy or an EGFR inhibitor.
  • Enrollment is expected to take approximately 15 months (9 months for dose escalation, 6 months for expansion). Completion of active treatment and post treatment follow-up is expected to take 6 - 12 additional months.
  • dose level 1 If unacceptable toxicity occurs at dose level 1 , only one dose reduction for each drug is allowed: Compound 1 10 mg, erlotinib 75 mg, and oral azacitidine 100 mg. [00330] Dose levels 2a and 2b and dose levels 3a and 3b have comparable dose intensity and may be enrolled concurrently.
  • Treatment is administered in 28-day cycles.
  • Compound 1 and erlotinib will be dosed daily in Arm A; oral azacitidine will be dosed concurrent with daily Compound 1 for the first 21 of 28 days in Arm B; oral azacitidine will be dosed only for 7 days before dosing with Compound 1 alone for 21 of 28 days in Arm C.
  • slight modifications to the dosing schedule will occur prior to and during Cycle 1 in order to facilitate PK and PD evaluation of each drug alone and in combination.
  • Administration of study drugs is described below:
  • Combined administration with Compound 1 will start on Day 2. Oral azacitidine will continue through Day 21 and Compound 1 through Day 28.
  • oral azacitidine will be administered on Day 1 through 7 and Compound 1 will be administered on Day 8 through 28.
  • Study drugs are taken together at approximately the same time each morning. Due to a significant interaction of erlotinib with food, subjects in Arm A must take study drugs on an empty stomach at least 1 hour before and 2 hours after eating. There are no such food restrictions for subjects taking Compound 1 or oral azacitidine in Arms B and C.
  • Study treatment may be discontinued if there is evidence of disease progression, unacceptable toxicity or subject/physician decision to withdraw. Subjects may continue to receive study drugs beyond disease progression at the discretion of the Investigator.
  • the estimated total number of subjects to be enrolled during dose escalation is 54 to 108, depending on cohort size. Approximately 30 additional subjects (10 per regimen) will be evaluated for safety, PK, PD and preliminary antitumor effects during the expansion phase.
  • Subjects will be evaluated for efficacy after every 2 cycles through Cycle 6 and every 3 cycles thereafter. All treated subjects will be included in the efficacy analysis.
  • the primary efficacy variable is tumor response rate and by progression- free survival at the end of 4 cycles of treatment. Tumor response will be determined by the Investigator, based on Response Evaluation Criteria in Solid Tumors (RECIST 1.1; Eisenhauer E.A., Therasse P., Bogaerts J., et al. New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1).
  • Secondary and exploratory endpoints include evaluation of mTOR, EGFR, and oral azacitidine biomarkers in blood and/or tumor and exploration of PK, PD, toxicity, and activity relationships.
  • the safety variables for this study are adverse events (AEs), safety clinical laboratory variables, 12-lead electrocardiograms (ECGs), left ventricular ejection fraction (LVEF) assessments, physical examinations, vital signs, exposure to study treatment, assessment of concomitant medications, and pregnancy testing for females of child bearing potentials (FCBP).
  • AEs adverse events
  • ECGs 12-lead electrocardiograms
  • LVEF left ventricular ejection fraction
  • FCBP pregnancy testing for females of child bearing potentials
  • the SRC will also select the dose and schedule of Compound 1 in combination with erlotinib and oral azacitidine appropriate for cohort expansion.
  • One or both schedules of Compound 1 and oral azacitidine may be selected for cohort expansion.
  • the SRC will continue to review safety data regularly throughout the study and make recommendations about study continuation and dose modification, as appropriate.
  • the concentration-time profiles of Compound 1, Ml, erlotinib and oral azacitidine will be determined from serial blood samples collected after administration of study drugs as single agents and after combination treatment.
  • the pharmacokinetics (PK) of Compound 1 and azacitidine will be determined after oral administration of each drug as a single agent and after combination treatment (Compound 1/oral azacitidine) using: (1) Maximum observed
  • C max concentration in plasma
  • AUC Area under the concentration-time curve
  • t max Time to maximum concentration
  • Ti /2 Terminal half-life
  • Vz/F Apparent volume of distribution
  • combination with erlotinib or oral azacitidine will be correlated with safety, PD and activity outcomes.
  • the principal metabolites of Compound I, including Ml, will be quantified in plasma.
  • the PK of the Ml metabolite after oral administration of Compound I as a single agent and in combination with erlotinib or oral azacitidine will be characterized.
  • Biomarker evaluation will include analysis of mTOR pathway biomarkers, and other signaling pathways when possible, in blood and tumor after both single agent and combination treatment. In some instances, the changes of each biomarker will be determined by comparing the levels of biomarkers in pre- and on-treatment samples and, where possible, correlate these with PK findings and tumor response over time. [00344] Assessment of gene DNA methylation and expression status in blood and tumor
  • Tumor gene sequencing will be performed at baseline on archival or Screening tumor biopsies to test for multiple genomic abnormalities.
  • Inclusion criteria for the study are: (1) Men and women, 18 years or older, with histologically or cytologically-confirmed, Stage IIIB/IV Non-Small Cell Lung Cancer with tumor progression following at least one prior treatment regimen (either chemotherapy or an Epidermal Growth Factor Receptor inhibitor for advanced disease), (2) Eastern Cooperative Oncology Group Performance Score of 0 or 1, (3) the following laboratory values: Absolute Neutrophil Count (ANC) > 1.0 x 10 9 /L; hemoglobin (Hgb) > 9 g/dL; platelets (pit) > 100 x 10 9 /L; potassium within normal limits or correctable with supplements; AST/SGOT and ALT/SGPT ⁇ 2.5 x Upper Limit of Normal (ULN) or ⁇ 5.0 x ULN if liver tumor is present; serum bilirubin ⁇ 1.5 x ULN; estimated serum creatinine clearance of > 60 mL/min/ 1.73m 2 using the Cockcroft-Gault equation; subjects who complete Cycle
  • Exclusion criteria for the study are: (1) Prior systemic cancer-directed treatments or investigational drugs within 4 wks or 5 half lives, whichever is shorter, (2) Symptomatic central nervous system metastases, (3) Known acute or chronic pancreatitis, (4) Subjects with persistent diarrhea or malabsorption > NCI CTCAE grade 2, despite medical management,
  • Impaired cardiac function or significant cardiac disease including any of the following: LVEF ⁇ 45% as determined by MUGA or ECHO; complete left bundle branch or bifascicular block; congenital long QT syndrome; persistent or clinically meaningful ventricular arrhythmias; QTcF > 460 msec on Screening ECG (mean of triplicate recordings); unstable angina pectoris or myocardial infarction ⁇ 3 months prior to starting study drugs; uncontrolled hypertension (blood pressure > 160/95 mmHg); (6) Diabetes on active treatment with either of the following: Fasting blood glucose (FBG) >126 mg/dL (7.0 mmol/L) or HbAlc > 6.5%, (7) Known Human
  • Immunodeficiency Virus infection chronic active hepatitis B or C virus infection, (8) Prior treatment with an investigational dual TORC1/TORC2, PI3K, or AKT inhibitor, (9) Major surgery ⁇ 2 weeks prior to starting study drugs; no specific wash out is required for radiotherapy. Subjects must have recovered from any effects of recent therapy that might confound the safety evaluation of study drug, (10) Women who are pregnant or breast feeding. Adults of reproductive potential not employing two forms of birth control, and (11) history of concurrent second cancers requiring ongoing systemic treatment.
  • patients undergoing the clinical protocol provided herein have shown, or will show a positive tumor response, such as inhibition of tumor growth or a reduction in tumor size.
  • patients undergoing the clinical protocol provided herein achieved, or will achieve a Response Evaluation Criteria in Solid Tumors (for example, RECIST 1.1) of complete response, partial response or stable disease after
  • patients undergoing the clinical protocol provided herein have shown or will show increased survival without tumor progression.
  • patients undergoing the clinical protocol provided herein have shown or will show inhibition of disease progression, inhibition of tumor growth, reduction of primary tumor, relief of tumor-related symptoms, inhibition of tumor secreted factors (including tumor secreted hormones, such as those that contribute to carcinoid syndrome), delayed appearance of primary or secondary tumors, slowed development of primary or secondary tumors, decreased occurrence of primary or secondary tumors, slowed or decreased severity of secondary effects of disease, arrested tumor growth and regression of tumors, increased Time To Progression (TTP), increased Progression Free Survival (PFS), and/or increased Overall Survival (OS), among others.
  • TTP Time To Progression
  • PFS Progression Free Survival
  • OS Overall Survival
  • a gene was considered to be mutant (variant) if it showed one of the following: mutation(s), for example, likely or known somatic variants; variants of unknown significance; or structural variation (deletion, amplification or rearrangement).
  • a gene was considered to be wild type when no sequencing alterations are detected for this gene.
  • a gene cluster is considered to be mutated if any gene in the cluster is mutated as defined above;
  • Progression-Free Survival was calculated as the time from first dose date to disease progression or death, whichever occurred first. Disease progression is determined by RECIST Version 1.1 criteria for solid tumor subjects, and IWC criteria for DLBCL. Within a tumor type and for selected genes, the Kaplan-Meier estimate of median PFS with its two-sided 95% CI was provided for each mutation group (mutant versus wild type) of that given gene. The Kaplan-Meier plots of progression free survival by cohort were presented. The raw P-value of the log rank test comparing survival distribution of PFS between mutant and wild type was provided.
  • OS overall survival
  • Subjects who has no death reported will be censored at the last contact date the subject is known to be alive or the clinical cut-off date whichever is earlier.
  • a Wilcoxon-Mann- Whitney test was conducted to compare tumor shrinkage between wild type and mutant subjects for selected genes within a given tumor type. The raw p-value of the Wilcoxon test was provided. Genes with corresponding p-values ⁇ 0.05 were noted.
  • DNA sequencing data are regarded as baseline characteristics and they are considered not to change after treatment.
  • the endpoint are binary defined as wild type (WT) or mutated (MUT).
  • WT wild type
  • MUT mutated
  • a gene is considered to be "WT' when no mutation is detected for this gene.
  • a gene is considered to be "MUT” if it has structure variant (SV, copy number variation or rearrangement), no matter whether it has localized variant(s) and what type(s) of localized variant(s) it has.
  • variants in the following genes are associated with response status accessed through RECIST or IWC.
  • variants in ARID1A, and/or CEBPA are associated with response status accessed through RECIST or IWC.
  • variants in one or more of ARID1A, FGFR2, IGF1R, RICTOR, and STK11 are associated with response status accessed through RECIST or IWC.
  • variants in the following genes are associated with disease control status accessed through RECIST or IWC.
  • variants in GPR124 are associated with disease control status accessed through RECIST or IWC.
  • variants in GPR124 are associated with disease control status accessed through RECIST or IWC.
  • variants in the following genes are associated with target lesion tumor shrinkage.
  • variants in TNFAIP3 are associated with target lesion tumor shrinkage.
  • variants in the following genes are associated with PFS.
  • NSCLC variants in one or more of APC, ARIDIA, CARDl 1, FANCA, and KIT are associated with PFS.
  • variants in JAK2 are associated with PFS.
  • variants in BRAF are associated with PFS.
  • A549 was used as a control cell line. A549 was purchased from National Cancer Institute (NCI) and cultured in RPMI + 10% fetal bovine serum (FBS).
  • NCI National Cancer Institute
  • FBS 10% fetal bovine serum
  • ATCC American Type Culture Collection
  • BME ⁇ -mercaptoethanol
  • DSMZ ⁇ -mercaptoethanol
  • Reverse Phase Protein Array Cell pellets were made for 37 cell lines without any compound treatment and a reverse phase protein array (RPPA) was performed as described in Tibes R, et al. Mol Cancer Ther 2006;5:2512-2521. The RPPA analysis of the 37 hematological cell lines was performed with 262 antibodies. The relative level of each protein in each sample was determined and normalized for protein loading. Protein levels were then transformed to log2 values and median centered by individual batch.
  • RPPA reverse phase protein array
  • RNA was isolated using RNeasy. Double-stranded cDNA and biotin-labeled cRNA were synthesized using 100 ng of total RNA using Ambion's MessageAmp Premier RNA Amplification Kit. Biotin-labeled complementary RNA (cRNA), at 15 ⁇ g, was fragmented and hybridized to each GeneChip Human Genome U133 Plus 2.0 Array. Arrays were then washed by the use of Affymetrix fluidics stations and scanned with the GeneChip
  • RLT RNeasy kit tissue lysis
  • cRNA Biotin-labeled complementary RNA
  • Compound 1 concentrations of Compound 1 (0.5 nM to 10 ⁇ ) were spotted in a 10-point serial dilution fashion (3-fold dilution) in duplicate within the plate via an acoustic dispenser (EDCATS-100) into an empty 384-well plate.
  • the dimethyl sulfoxide (DMSO) concentration was kept constant for a final assay concentration of 0.1% DMSO. Plates were replicated for use against different cell lines and testing periods. After compound plate replication, all plates were sealed (Agilent ThermoLoc) and stored at -20 °C for up to 1 month.
  • a control cell line (A549) was included in each of the assays. The response of the control cell line to the compound was monitored closely to enable comparison of the data generated through the assay period. All data were normalized and presented as a percentage of the growth in DMSO-treated cells. Results were then expressed as a GI 50 value, which is the compound concentration required to inhibit cell growth in treated cells to 50% of the growth of the untreated control cells during the 72 hours of treatment. The GI 50 value corrects for the cell count at time zero. In addition, the IC 50 value of Compound 1 for each cell line was calculated.
  • Figure 6 shows that the sensitivity to Compound 1 correlated with activation of mTORCl and mTORC2 in a subgroup of DLBCL lines, as measured via biomarker RPPA (pmTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, pS6 S240/S244 and S235/S236).
  • biomarker RPPA pmTOR S2448, p-p70S6K T389, pGSK3b S9 and S21, pAKT S473 and T308, pTSC2 T1462, pS6 S240/S244 and S235/S236).

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